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7nst

ColicinE9 partial translocation complex

Method: ELECTRON MICROSCOPY Dmax: 167.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Outer membrane protein F

Escherichia coli (strain K12)

UniProt P02931

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 23–362 Chain B； UniProt 23–362 Chain C； UniProt 23–362 Not recorded Colicin-E9 × 1 （P09883） Tol-Pal system protein TolB × 1 （A0A6D2XIU5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7NST Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BT9 OMPF PORIN MUTANT D74A Deposited 1998-09-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：D74A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 3.00 Å R-free 0.269
1GFM OMPF PORIN (MUTANT D113G) Deposited 1996-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：D113G C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å
1GFN OMPF PORIN DELETION (MUTANT DELTA 109-114) Deposited 1996-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：DEL(109-114) C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.10 Å
1GFO OMPF PORIN (MUTANT R132P) Deposited 1996-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：R132P C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.30 Å
1GFP OMPF PORIN (MUTANT R42C) Deposited 1996-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：R42C C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1GFQ OMPF PORIN (MUTANT R82C) Deposited 1996-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：R82C C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1HXT OMPF PORIN MUTANT NQAAA Deposited 2001-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：R42A,R82A,D113N,E117Q,R132A C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 30 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.289
1HXU OMPF PORIN MUTANT KK Deposited 2001-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：V18K,G131K No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.264
1HXX OMPF PORIN MUTANT Y106F Deposited 2001-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：Y106F C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 12 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.249
1MPF STRUCTURAL AND FUNCTIONAL ALTERATIONS OF A COLICIN RESISTANT MUTANT OF OMPF-PORIN FROM ESCHERICHIA COLI Deposited 1994-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å
1OPF THE STRUCTURE OF OMPF PORIN IN A TETRAGONAL CRYSTAL FORM Deposited 1994-11-21 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Chain B 23–362（340 aa）
Chain C 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å
1OPF THE STRUCTURE OF OMPF PORIN IN A TETRAGONAL CRYSTAL FORM Deposited 1994-11-21 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 23–362（340 aa）
Chain E 23–362（340 aa）
Chain F 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å
2OMF OMPF PORIN Deposited 1995-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 36 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å
2ZFG Structure of OMPF PORIN Deposited 2008-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded MG MAGNESIUM ION × 3 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.59 Å R-free 0.218
2ZLD Structure of OmpF co-crystallized with T83 Deposited 2008-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.294
2ZLD Structure of OmpF co-crystallized with T83 Deposited 2008-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.294
2ZLD Structure of OmpF co-crystallized with T83 Deposited 2008-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 23–362（340 aa）
Chain B 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.294
3FYX The Structure of OmpF porin with a synthetic dibenzo-18-crown-6 as modulator Deposited 2009-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Mutation：K16C 451 N-(6,7,9,10,17,18,20,21-octahydrodibenzo[b,k][1,4,7,10,13,16]hexaoxacyclooctadecin-2-yl)acetamide × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.2 M CaCl2, 48% PEG 400, 0.1 M Na-HEPES, pH 7.5, VAPOR DIFFUSION, temperature 291K
Resolution 3.40 Å R-free 0.294
3HW9 Cation selective pathway of OmpF porin revealed by anomalous x-ray diffraction Deposited 2009-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–362（362 aa）
Not recorded P6G HEXAETHYLENE GLYCOL × 3 K POTASSIUM ION × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.5M NaCl, Na Phosphate pH 6.5, 0.9% BOG, 0.09% octylPOE and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.61 Å R-free 0.300
3HW9 Cation selective pathway of OmpF porin revealed by anomalous x-ray diffraction Deposited 2009-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–362（362 aa）
Not recorded P6G HEXAETHYLENE GLYCOL × 3 K POTASSIUM ION × 9 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.5M NaCl, Na Phosphate pH 6.5, 0.9% BOG, 0.09% octylPOE and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.61 Å R-free 0.300
3HW9 Cation selective pathway of OmpF porin revealed by anomalous x-ray diffraction Deposited 2009-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa）
Chain B 1–362（362 aa）
Not recorded P6G HEXAETHYLENE GLYCOL × 2 K POTASSIUM ION × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.5M NaCl, Na Phosphate pH 6.5, 0.9% BOG, 0.09% octylPOE and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.61 Å R-free 0.300
3HWB Cation selective pathway of OmpF porin revealed by anomalous diffraction Deposited 2009-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–362（362 aa）
Not recorded RB RUBIDIUM ION × 42 P6G HEXAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.5M NaCl,Na Phosphate buffer pH 6.5, 0.9% BOG, 0.09% octylPOE, sodium azide and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.00 Å R-free 0.285
3HWB Cation selective pathway of OmpF porin revealed by anomalous diffraction Deposited 2009-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–362（362 aa）
Not recorded RB RUBIDIUM ION × 15 P6G HEXAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.5M NaCl,Na Phosphate buffer pH 6.5, 0.9% BOG, 0.09% octylPOE, sodium azide and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.00 Å R-free 0.285
3HWB Cation selective pathway of OmpF porin revealed by anomalous diffraction Deposited 2009-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–362（362 aa）
Chain B 1–362（362 aa）
Not recorded RB RUBIDIUM ION × 19 P6G HEXAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.5M NaCl,Na Phosphate buffer pH 6.5, 0.9% BOG, 0.09% octylPOE, sodium azide and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.00 Å R-free 0.285
3K19 OmpF porin Deposited 2009-09-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：sequence database residues 1-340
Chain B 23–362（340 aa） Fragment：sequence database residues 1-340
Chain C 23–362（340 aa） Fragment：sequence database residues 1-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.2M sodium chloride, 0.1M Imidazole pH 8, VAPOR DIFFUSION, temperature 293K
Resolution 3.79 Å R-free 0.288
3K19 OmpF porin Deposited 2009-09-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 23–362（340 aa） Fragment：sequence database residues 1-340
Chain E 23–362（340 aa） Fragment：sequence database residues 1-340
Chain F 23–362（340 aa） Fragment：sequence database residues 1-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.2M sodium chloride, 0.1M Imidazole pH 8, VAPOR DIFFUSION, temperature 293K
Resolution 3.79 Å R-free 0.288
3K19 OmpF porin Deposited 2009-09-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain G 23–362（340 aa） Fragment：sequence database residues 1-340
Chain H 23–362（340 aa） Fragment：sequence database residues 1-340
Chain I 23–362（340 aa） Fragment：sequence database residues 1-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.2M sodium chloride, 0.1M Imidazole pH 8, VAPOR DIFFUSION, temperature 293K
Resolution 3.79 Å R-free 0.288
3K19 OmpF porin Deposited 2009-09-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain J 23–362（340 aa） Fragment：sequence database residues 1-340
Chain K 23–362（340 aa） Fragment：sequence database residues 1-340
Chain L 23–362（340 aa） Fragment：sequence database residues 1-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.4 M NaH2PO4/1.6 M K2HPO4, 0.2M sodium chloride, 0.1M Imidazole pH 8, VAPOR DIFFUSION, temperature 293K
Resolution 3.79 Å R-free 0.288
3K1B Structure of OmpF porin Deposited 2009-09-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：sequence database residues 1-340
Chain B 23–362（340 aa） Fragment：sequence database residues 1-340
Chain C 23–362（340 aa） Fragment：sequence database residues 1-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 3.9；293 K；0.48 sodium phosphate monobasic, 0.72 M potassium phosphate monobasic, 0.1 M acetate pH 3.9, VAPOR DIFFUSION, temperature 293K
Resolution 4.39 Å R-free 0.329
3K1B Structure of OmpF porin Deposited 2009-09-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 23–362（340 aa） Fragment：sequence database residues 1-340
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 3.9；293 K；0.48 sodium phosphate monobasic, 0.72 M potassium phosphate monobasic, 0.1 M acetate pH 3.9, VAPOR DIFFUSION, temperature 293K
Resolution 4.39 Å R-free 0.329
4D5U Structure of OmpF in I2 Deposited 2014-11-07 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Chain B 23–362（340 aa）
Chain C 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；16% PEG 4000, 0.4 M NACL AND 10 MM CDCL2 AS AN ADDITIVE, pH 8
Resolution 3.50 Å R-free 0.283
4D5U Structure of OmpF in I2 Deposited 2014-11-07 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 23–362（340 aa）
Chain E 23–362（340 aa）
Chain F 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；16% PEG 4000, 0.4 M NACL AND 10 MM CDCL2 AS AN ADDITIVE, pH 8
Resolution 3.50 Å R-free 0.283
4GCP Crystal Structure of E. coli OmpF porin in complex with Ampicillin Deposited 2012-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：UNP Residues 23-362
Not recorded AIC (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.98 Å R-free 0.239
4GCP Crystal Structure of E. coli OmpF porin in complex with Ampicillin Deposited 2012-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa） Fragment：UNP Residues 23-362
Not recorded AIC (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.98 Å R-free 0.239
4GCQ Crystal Structure of E. coli OmpF porin in complex with Carbenicillin Deposited 2012-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：UNP Residues 23-362
Not recorded 0JM (2S,5R,6R,7R)-6-{[(2R)-2-carboxy-2-phenylacetyl]amino}-7-hydroxy-3,3-dimethyl-4-thia-1-azabicyclo[3.2.0]heptane-2-carbo xylic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.20 Å R-free 0.275
4GCQ Crystal Structure of E. coli OmpF porin in complex with Carbenicillin Deposited 2012-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa） Fragment：UNP Residues 23-362
Not recorded 0JM (2S,5R,6R,7R)-6-{[(2R)-2-carboxy-2-phenylacetyl]amino}-7-hydroxy-3,3-dimethyl-4-thia-1-azabicyclo[3.2.0]heptane-2-carbo xylic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.20 Å R-free 0.275
4GCS Crystal Structure of E. coli OmpF porin in complex with Ertapenem Deposited 2012-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：UNP Residues 23-362
Not recorded 1RG (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.87 Å R-free 0.227
4GCS Crystal Structure of E. coli OmpF porin in complex with Ertapenem Deposited 2012-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa） Fragment：UNP Residues 23-362
Not recorded 1RG (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.87 Å R-free 0.227
4JFB Crystal structure of OmpF in C2 with tNCS Deposited 2013-02-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Chain B 23–362（340 aa）
Chain C 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18-22% PEG 1500, 5-10% 2-Methyl-2,4-pentanediol, 0.1M Tris-HCl pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.80 Å R-free 0.314
4JFB Crystal structure of OmpF in C2 with tNCS Deposited 2013-02-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 23–362（340 aa）
Chain E 23–362（340 aa）
Chain F 23–362（340 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；18-22% PEG 1500, 5-10% 2-Methyl-2,4-pentanediol, 0.1M Tris-HCl pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.80 Å R-free 0.314
4LSE Ion selectivity of OmpF porin soaked in 0.2M NaBr Deposited 2013-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：UNP residues 23-362
Chain B 23–362（340 aa） Fragment：UNP residues 23-362
Chain C 23–362（340 aa） Fragment：UNP residues 23-362
Not recorded BR BROMIDE ION × 8 MG MAGNESIUM ION × 6 PEG DI(HYDROXYETHYL)ETHER × 4 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.10 Å R-free 0.290
4LSF Ion selectivity of OmpF soaked in 0.1M KBr Deposited 2013-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：UNP residues 23-362
Not recorded BR BROMIDE ION × 9 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.90 Å R-free 0.298
4LSF Ion selectivity of OmpF soaked in 0.1M KBr Deposited 2013-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa） Fragment：UNP residues 23-362
Not recorded BR BROMIDE ION × 12 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 1.90 Å R-free 0.298
4LSH Ion selectivity of OmpF porin soaked in 0.2M KBr Deposited 2013-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：UNP residues 23-362
Not recorded BR BROMIDE ION × 18 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, crystals soaked in 0.2 M potassium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.20 Å R-free 0.293
4LSH Ion selectivity of OmpF porin soaked in 0.2M KBr Deposited 2013-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa） Fragment：UNP residues 23-362
Not recorded BR BROMIDE ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, crystals soaked in 0.2 M potassium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.20 Å R-free 0.293
4LSI Ion selectivity of OmpF porin soaked in 0.3M KBr Deposited 2013-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa） Fragment：UNP residues 23-362
Chain B 23–362（340 aa） Fragment：UNP residues 23-362
Chain C 23–362（340 aa） Fragment：UNP residues 23-362
Not recorded PEG DI(HYDROXYETHYL)ETHER × 9 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 4 GOL GLYCEROL × 4 MG MAGNESIUM ION × 8 BR BROMIDE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, crystals soaked in 0.3 M potassium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.09 Å R-free 0.245
5NUO Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 23–362（340 aa）
Chain C 23–362（340 aa）
Chain E 23–362（340 aa）
Not recorded SO4 SULFATE ION × 6 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400
Resolution 3.20 Å R-free 0.269
5NUQ Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 23–362（340 aa）
Chain C 23–362（340 aa）
Chain E 23–362（340 aa）
Not recorded C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.32 M lithium chloride 0.1M Sodium citrate pH 5.5 and 14% PEG 400
Resolution 3.20 Å R-free 0.306
5NUQ Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 23–362（340 aa）
Chain D 23–362（340 aa）
Chain F 23–362（340 aa）
Not recorded C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.32 M lithium chloride 0.1M Sodium citrate pH 5.5 and 14% PEG 400
Resolution 3.20 Å R-free 0.306
5NUR Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 23–362（340 aa）
Chain C 23–362（340 aa）
Chain E 23–362（340 aa）
Not recorded CA CALCIUM ION × 3 SO4 SULFATE ION × 8 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400
Resolution 3.29 Å R-free 0.259
6WTZ Cryo-EM structure of E. Coli OmpF Deposited 2020-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–362（362 aa）
Chain B 1–362（362 aa）
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
6ZHP Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic Deposited 2020-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 3 QLB 2-[2-(2-octoxyethoxy)ethoxy]ethanol × 6 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；22 % PEG 2000, 0.25 M MgCl2, 0.1 M Tris
Resolution 2.05 Å R-free 0.207
6ZHV Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic Deposited 2020-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–362（362 aa）
Chain B 1–362（362 aa）
Chain C 1–362（362 aa）
Not recorded MG MAGNESIUM ION × 3 NA SODIUM ION × 12 QLB 2-[2-(2-octoxyethoxy)ethoxy]ethanol × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；50% PEG 200, 0.2 M MgCl2, 0.1 M NaCacodylate
Resolution 1.95 Å R-free 0.233
7NSU ColicinE9 intact translocation complex Deposited 2021-03-08 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 23–362（340 aa）
Chain B 23–362（340 aa）
Chain C 23–362（340 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane
Resolution 4.70 Å
8C7L Serendipitous structure of OmpF contaminant in space group P21. Deposited 2023-01-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–362（362 aa）
Chain B 1–362（362 aa）
Chain C 1–362（362 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1mM NaCl, 0.1 MgCl2, 0.1 mM NaAcetate pH 4.5, 30% PEG400 copurified after refolding with 0.2 % lauryl sulfobetaine
Resolution 3.52 Å R-free 0.255
8C7L Serendipitous structure of OmpF contaminant in space group P21. Deposited 2023-01-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 1–362（362 aa）
Chain E 1–362（362 aa）
Chain F 1–362（362 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1mM NaCl, 0.1 MgCl2, 0.1 mM NaAcetate pH 4.5, 30% PEG400 copurified after refolding with 0.2 % lauryl sulfobetaine
Resolution 3.52 Å R-free 0.255
9J9L artificial mononuclear Zn-bound metalloprotein 1 (M1:Zn) Deposited 2024-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded ZN ZINC ION × 3 BCN BICINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Bicine pH 8.0, and 28 % w/v PEG 2000
Resolution 2.60 Å R-free 0.278
9J9M artificial mononuclear Zn-bound metalloprotein 1 (M1:Mn) Deposited 2024-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Resolution 2.29 Å R-free 0.221
9J9M artificial mononuclear Zn-bound metalloprotein 1 (M1:Mn) Deposited 2024-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa）
Not recorded MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Resolution 2.29 Å R-free 0.221
9J9N artificial mononuclear Zn-bound metalloprotein 2 (M2:Zn) Deposited 2024-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Resolution 2.86 Å R-free 0.250
9J9N artificial mononuclear Zn-bound metalloprotein 2 (M2:Zn) Deposited 2024-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Resolution 2.86 Å R-free 0.250
9J9O artificial dinuclear Zn-bound metalloprotein 1 (D1:2Zn) Deposited 2024-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Resolution 2.99 Å R-free 0.239
9J9O artificial dinuclear Zn-bound metalloprotein 1 (D1:2Zn) Deposited 2024-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 23–362（340 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000
Resolution 2.99 Å R-free 0.239
9J9P artificial mononuclear Zn-bound metalloprotein 3 (M3:Zn) Deposited 2024-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 23–362（340 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.3 M MgCl2, MOPS pH 8.0, and 28 % w/v PEG 2000
Resolution 3.47 Å R-free 0.266

41 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OMPF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–340； UniProt 23–362 Author chain B； PDBConstruct 1–340； UniProt 23–362 Author chain C； PDBConstruct 1–340； UniProt 23–362

Colicin-E9

Escherichia coli

UniProt P09883

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain D； UniProt 1–314 Mutation：A33C Outer membrane protein F × 3 （P02931） Tol-Pal system protein TolB × 1 （A0A6D2XIU5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7NST Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BXI CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 Deposited 1998-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 449–582（134 aa） Fragment：DNASE DOMAIN, RESIDUES 450-581
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；24%(W/V)PEG 4K, 0.1MM SODIUM-ACETATE, PH5.3
Resolution 2.05 Å R-free 0.315
1EMV CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS) Deposited 2000-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% PEG 4000, 0.1M sodium acetate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.260
1FR2 CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN IM9(E41A) Deposited 2000-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% PEG 4000, 0.1M sodium acetate, , pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.232
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 1.80 Å R-free 0.222
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 1.80 Å R-free 0.222
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 1.80 Å R-free 0.222
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 1.80 Å R-free 0.222
1V13 CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 450–582（133 aa）
Chain B 450–582（133 aa）
Mutation：YES Mutation：YES ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.8；pH 5.80
Resolution 2.00 Å R-free 0.307
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.90 Å R-free 0.306
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.90 Å R-free 0.306
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.90 Å R-free 0.306
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.90 Å R-free 0.306
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.40 Å R-free 0.329
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.40 Å R-free 0.329
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain C 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.40 Å R-free 0.329
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582
Mutation：YES ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 2.40 Å R-free 0.329
2GYK Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A) Deposited 2006-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.232
2GYK Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A) Deposited 2006-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.232
2GZE Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A) Deposited 2006-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：Colicin E9,C-terminal Domain,DNase Domain
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOUR DIFFUSSION,SITTING DROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Resolution 1.80 Å R-free 0.242
2GZF Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y54F) Deposited 2006-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：Colicin E9,C-terminal Domain,DNase Domain
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOUR DIFFUSSION,SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOUR DIFFUSSION,SITTING DROP, temperature 277K
Resolution 1.75 Å R-free 0.222
2GZG Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (Y55F) Deposited 2006-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Resolution 1.70 Å R-free 0.204
2GZI Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (V34A) Deposited 2006-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Resolution 1.70 Å R-free 0.256
2GZJ Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A) Deposited 2006-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Resolution 1.60 Å R-free 0.232
2GZJ Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A) Deposited 2006-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN
Not recorded ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Resolution 1.60 Å R-free 0.232
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5
Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5
Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5
Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5
Resolution 2.00 Å R-free 0.222
2K5X Chemical shift structure of COLICIN E9 DNASE domain with its cognate immunity protein IM9 Deposited 2008-07-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：UNP residues 450-582
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.2；298 K
Resolution not provided
2VLN N75A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582
Mutation：YES MLA MALONIC ACID × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å R-free 0.203
2VLO K97A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582
Mutation：YES SO4 SULFATE ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å R-free 0.228
2VLP R54A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582
Mutation：YES MLA MALONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 2.9 M AMMONIUM SULPHATE AND 100 MM BIS-TRIS PH 5.5
Resolution 2.00 Å R-free 0.229
2VLQ F86A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582
Mutation：YES MLA MALONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 2.9 M AMMONIUM SULPHATE AND 100 MM BIS-TRIS PH 5.5
Resolution 1.60 Å R-free 0.199
2WPT The crystal structure of Im2 in complex with colicin E9 DNase Deposited 2009-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 450–582（133 aa）
Mutation：YES GOL GLYCEROL × 2 NO3 NITRATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；pH 6.8
Resolution 1.78 Å R-free 0.223
3O0E Crystal structure of OmpF in complex with colicin peptide OBS1 Deposited 2010-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 2–18（17 aa） Fragment：UNP Residues 2-18
Chain N 2–18（17 aa） Fragment：UNP Residues 2-18
Chain P 2–18（17 aa） Fragment：UNP Residues 2-18
Not recorded BOG octyl beta-D-glucopyranoside × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2M Li2SO4, 0.1M sodium cacodylate, pH 6.5, sitting drop vapor diffusion, temperature 293K
Resolution 3.01 Å R-free 0.302
3O0E Crystal structure of OmpF in complex with colicin peptide OBS1 Deposited 2010-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain M 2–18（17 aa） Fragment：UNP Residues 2-18
Chain O 2–18（17 aa） Fragment：UNP Residues 2-18
Chain Q 2–18（17 aa） Fragment：UNP Residues 2-18
Not recorded BOG octyl beta-D-glucopyranoside × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2M Li2SO4, 0.1M sodium cacodylate, pH 6.5, sitting drop vapor diffusion, temperature 293K
Resolution 3.01 Å R-free 0.302
4JML Crystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) complex. Deposited 2013-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 32–47（16 aa） Fragment：T-domain, Residues 32-47
Mutation：A33C CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；80mM calcium chloride, 24% PEG 5000MME, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.226
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–582（582 aa）
Mutation：Y324C, L447C, D448A, K449M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350
Resolution 3.20 Å R-free 0.271
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–582（582 aa）
Mutation：Y324C, L447C, D448A, K449M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350
Resolution 3.20 Å R-free 0.271
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–582（582 aa）
Mutation：Y324C, L447C, D448A, K449M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350
Resolution 3.20 Å R-free 0.271
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–582（582 aa）
Mutation：Y324C, L447C, D448A, K449M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350
Resolution 3.20 Å R-free 0.271
7NSU ColicinE9 intact translocation complex Deposited 2021-03-08 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–582（582 aa）
Mutation：A33C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane
Resolution 4.70 Å

24 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CEA9_ECOLX
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–314； UniProt 1–314

Tol-Pal system protein TolB

Escherichia coli (strain K12)

UniProt A0A6D2XIU5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain E； UniProt 1–430 Mutation：P201C Outer membrane protein F × 3 （P02931） Colicin-E9 × 1 （P09883） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7NST Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7NSU ColicinE9 intact translocation complex Deposited 2021-03-08 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–430（430 aa）
Mutation：P201C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane
Resolution 4.70 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A6D2XIU5_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–430； UniProt 1–430

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7nst

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7nst
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7nst
Deposition date deposition_date2021-03-08
Structure title titleColicinE9 partial translocation complex
Keywords keywordsbacteriocin complex, import-stalled, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.18 Å
Radius of gyration Rg (electron density) rg_electron42.60 Å
Forward intensity I(0) i0529232000.00
Molecular weight molecular_weight182120.0 kDa
Excluded volume excluded_volume225090 ų
Envelope volume envelope_volume311750 ų
Hydration-shell volume shell_volume64288 ų
Envelope diameter envelope_diameter175.5 Å
Shell Rg shell_rg45.23 Å
Envelope Rg envelope_rg42.07 Å
Shape Rg shape_rg42.55 Å
Total Rg total_rg42.91 Å
Total atoms total_atoms23373
Residues n_residues1703
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax167.5 Å
Rg (real space) rg_real42.41 Å
Rg uncertainty (real space) rg_real_error2.19 Å
I(0) (real space) i0_real5.2920e+08
I(0) uncertainty (real space) i0_real_error9.5620e+06
Rg (reciprocal space) rg_reciprocal42.18 Å
I(0) (reciprocal space) i0_reciprocal529100000.0000
Solution quality estimate total_estimate0.7913
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.8 Å
Skewness Skewness skewness0.610
Kurtosis Kurtosis kurtosis0.420
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85070000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.490; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.952
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)