5nur

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

Method: X-RAY DIFFRACTION D_max: 139.7 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)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 6 其他Polymer 3 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 23–362 Chain C； UniProt 23–362 Chain E； UniProt 23–362	Not recorded	ABC transporter permease × 3 （A0A0W8AQT6） ;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ; × 1 ;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ; × 1 ;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ; × 1 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

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 5NUR	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 ligand/ion 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 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 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 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 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 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 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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
6WTZ Cryo-EM structure of E. Coli OmpF Deposited 2020-05-04	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	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 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 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
7NST ColicinE9 partial translocation complex Deposited 2021-03-08	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	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 3.70 Å
7NSU ColicinE9 intact translocation complex Deposited 2021-03-08	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 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 C； PDBConstruct 1–340； UniProt 23–362 Author chain E； PDBConstruct 1–340； UniProt 23–362

ABC transporter permease

Klebsiella pneumoniae

UniProt A0A0W8AQT6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 6 其他Polymer 3 PDB declaration: hexameric（6） Consistent with protein copy count	Chain B； UniProt 18–253 Chain D； UniProt 18–253 Chain F； UniProt 18–253	Not recorded	Outer membrane protein F × 3 （P02931） ;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ; × 1 ;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ; × 1 ;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ; × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5NUR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5NUO Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 18–253（236 aa） Chain D 18–253（236 aa） Chain F 18–253（236 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
5NUP Structural basis for maintenance of bacterial outer membrane lipid asymmetry Deposited 2017-05-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 18–253（236 aa） Chain E 18–253（236 aa） Chain F 18–253（236 aa）	Not recorded	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 19 LMT DODECYL-BETA-D-MALTOSIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.04 M magnesium chloride hexahydrate, 0.05 M sodium chloride, 0.1 M HEPES pH7.5 and 32 % PEG400	Resolution 2.90 Å R-free 0.290

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0W8AQT6_KLEPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–236； UniProt 18–253 Author chain D； PDBConstruct 1–236； UniProt 18–253 Author chain F； PDBConstruct 1–236； UniProt 18–253

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5nur
Deposition date deposition_date	2017-05-01
Structure title title	Structural basis for maintenance of bacterial outer membrane lipid asymmetry
Keywords keywords	Outer membrane, lipid asymmetry, lipoprotein, phospholipid translocation, membrane protein; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	42.05 Å
Radius of gyration Rg (electron density) rg_electron	42.44 Å
Forward intensity I(0) i0	521377000.00
Molecular weight molecular_weight	182960.0 kDa
Excluded volume excluded_volume	226770 Å³
Envelope volume envelope_volume	311190 Å³
Hydration-shell volume shell_volume	63146 Å³
Envelope diameter envelope_diameter	146.2 Å
Shell Rg shell_rg	45.47 Å
Envelope Rg envelope_rg	42.77 Å
Shape Rg shape_rg	42.45 Å
Total Rg total_rg	42.54 Å
Total atoms total_atoms	12920
Residues n_residues	1615
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	139.7 Å
Rg (real space) rg_real	42.15 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	5.2140e+08
I(0) uncertainty (real space) i0_real_error	9.4990e+06
Rg (reciprocal space) rg_reciprocal	42.05 Å
I(0) (reciprocal space) i0_reciprocal	521300000.0000
Solution quality estimate total_estimate	0.8678
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.8 Å
Skewness Skewness skewness	0.432
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58020000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.698

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Outer membrane protein F
Molecular weight formula_weight	37114.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A,E
Atom count atom_count	12920

AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF

来源 Source

来源生物 organism	Escherichia coli (strain K12)
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ABC transporter permease
Molecular weight formula_weight	26364.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B,F

CASSSSGDRPQGRSDPLEGFNRTMFNFNFNVVDPYVLRPVAVAWRDYVPQPARNGLSNFTSNLEEPAVMVNYFLQGDPYKGMVHFTRFFLNTILGMGGLIDVAGMANPQLQRVEPHRFGSTLGHYGVGYGPYVQLPFYGSFTLRDEGGDMADGLYPVLSWLTWPMSIGKWAVEGIETRAQLLDSDGLLRQSSDPYILMREAYFQRHDFIANGGKLTPADNPNAQAIQDELKDIDSQ

来源 Source

来源生物 organism	Klebsiella pneumoniae
NCBI Class编号 ncbi_taxonomy_id	573
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 branched

Description description	;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ;
Molecular weight formula_weight	940.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ;
Molecular weight formula_weight	940.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	;3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose ;
Molecular weight formula_weight	720.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	3

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5nurA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	5nurC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

Domain ID domain_id	5nurE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	160 — Porin
Homologous superfamily homologous superfamily	10 — Porin

▶

8. Citations (1)

▶

Unit-cell length a length_a	190.550 Å
Unit-cell length b length_b	179.660 Å
Unit-cell length c length_c	133.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.290 Å
Low-resolution limit resolution_low	47.399 Å
R factor r_factor	0.2212
R_work r_work	0.2193
R_free r_free	0.2591

fit	/app/data/saxs_computation/nu/5nur/5nur.fit
pddf	/app/data/pr_computation/nu/5nur/5nur.pr.out
profile	/app/data/saxs_computation/nu/5nur/5nur.dat

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

1. Protein Identity and Related Structures Protein Identity & Related Structures

Outer membrane protein F

State in the Current Structure

Other States of the Same Protein in the Database

ABC transporter permease

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)