SAXSdb — 3gkl

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

Colicin-E9 immunity protein

Escherichia coli

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 446–576	Fragment：UNP residues 446-576 Mutation：T20A, N24D, T27A, S28T, V34D, V37I, E41G, K57E	Colicin-E7 × 1 （P13479） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；292 K；30% PEG 400, 0.1 CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.20 Å R-free 0.277
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 446–576	Fragment：UNP residues 446-576 Mutation：T20A, N24D, T27A, S28T, V34D, V37I, E41G, K57E	Colicin-E7 × 1 （P13479） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；292 K；30% PEG 400, 0.1 CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.20 Å R-free 0.277

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 3GKL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M08 Crystal structure of the unbound nuclease domain of ColE7 Deposited 2002-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 447–576（130 aa） Fragment：Nuclease Domain Chain B 447–576（130 aa） Fragment：Nuclease Domain	Not recorded	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；sodium phosphate, Sodium Chloride, zinc chloride, ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.10 Å R-free 0.240
1MZ8 CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION Deposited 2002-10-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 446–576（131 aa） Fragment：nuclease domain	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；PEG4000, sodium phosphate, ammonium acetate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.230
1MZ8 CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION Deposited 2002-10-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 446–576（131 aa） Fragment：nuclease domain	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；PEG4000, sodium phosphate, ammonium acetate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.230
1PT3 Crystal structures of nuclease-ColE7 complexed with octamer DNA Deposited 2003-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: octameric	Chain A 449–576（128 aa） Fragment：residues 449-576 Chain B 449–576（128 aa） Fragment：residues 449-576	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；298 K；2.5 mM EDTA, 12.5 mM Tris-HCl (pH 7.5), 0.1 M Ammonium Formate, and 10 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.50	Resolution 2.50 Å R-free 0.289
1UJZ Crystal structure of the E7_C/Im7_C complex; a computationally designed interface between the colicin E7 DNase and the Im7 Immunity protein Deposited 2003-08-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 446–573（128 aa） Fragment：residues 446-573	Mutation：K528Q, T539R, H569A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEGMME 2000, ammonium sulfate, Sodium Acetate, Glycerol, DMSO, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.270
1ZNS Crystal structure of N-ColE7/12-bp DNA/Zn complex Deposited 2005-05-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 444–576（133 aa） Fragment：nuclease domain	Mutation：H545E	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25mM Tris-HCl, 0.1M Ammonium chloride, 10.5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.287
1ZNV How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor Deposited 2005-05-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 444–576（133 aa） Fragment：Nuclease domain	Mutation：H545E	NI NICKEL (II) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；0.3M phosphate buffer, 50mM NaCl, 20% PEG550 MME, 10% glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.235
1ZNV How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor Deposited 2005-05-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 444–576（133 aa） Fragment：Nuclease domain	Mutation：H545E	NI NICKEL (II) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；0.3M phosphate buffer, 50mM NaCl, 20% PEG550 MME, 10% glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.235
2AXC Crystal structure of ColE7 translocation domain Deposited 2005-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–316（257 aa） Fragment：N-terminal Translocation domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1M Tris-HCl pH 8.5, 1.5M (NH4)2SO4, 12% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.208
2ERH Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7 DNAse and the Im7 immunity protein Deposited 2005-10-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 447–573（127 aa）	Mutation：N516T, N517Q, K525R, K528Q, T539Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；30% PEG 4K, 0.6M ammonium acetate, 50mM Na acetate, 25% glycerol, 5% DMSO, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.271
2IVH Crystal structure of the nuclease domain of ColE7 (H545Q mutant) in complex with an 18-bp duplex DNA Deposited 2006-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 449–576（128 aa） Fragment：NUCLEASE DOMAIN, RESIDUES 449-576	Mutation：YES	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1 MICRO L COMPLEX SOLUTION AND 1 MICRO L RESERVOIR SOLUTION CONSISTING OF 40 % MPD, 0.4 M AMMONIUM FORMATE AND 0.1 M ACETATE BUFFER (PH4.8) AT ROOM TEMPERATURE., pH 4.80	Resolution 2.80 Å R-free 0.265
2JAZ CRYSTAL STRUCTURE OF THE MUTANT N560D OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7 Deposited 2006-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 446–576（131 aa） Fragment：NUCLEASE DOMAIN, RESIDUES 446-576 Chain D 446–576（131 aa） Fragment：NUCLEASE DOMAIN, RESIDUES 446-576	Mutation：YES Mutation：YES	ZN ZINC ION × 4 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20 % W/V PEG3350 AND 0.1 M DI-AMMONIUM HYDROGEN CITRATE, pH 7.00	Resolution 2.03 Å R-free 0.249
2JB0 CRYSTAL STRUCTURE OF THE MUTANT H573A OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7 Deposited 2006-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 446–576（131 aa） Fragment：NUCLEASE DOMAIN, RESIDUES 446-576	Mutation：YES	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20 % W/V PEG3350 AND 0.2 M DI-AMMONIUM HYDROGEN CITRATE, pH 7.00	Resolution 1.91 Å R-free 0.250
2JBG crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7 Deposited 2006-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 446–576（131 aa） Fragment：NUCLEASE DOMAIN, RESIDUES 446-576 Chain D 446–576（131 aa） Fragment：NUCLEASE DOMAIN, RESIDUES 446-576	Mutation：YES Mutation：YES	ZN ZINC ION × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；20 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, 0.2 M AMMONIUM SULFATE, AND 0.1 M SODIUM ACETATE TRIHYDRATE AT PH 4.6	Resolution 2.20 Å R-free 0.249
3FBD Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA Deposited 2008-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 445–576（132 aa） Fragment：NUCLEASE DOMAIN	Mutation：D493Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG 3350, 16.25% MPD, 0.15M ammonium acetate, 0.025M sodium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.264
3FBD Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA Deposited 2008-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 445–576（132 aa） Fragment：NUCLEASE DOMAIN	Mutation：D493Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG 3350, 16.25% MPD, 0.15M ammonium acetate, 0.025M sodium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.264
3GJN Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 446–576（131 aa） Fragment：UNP residues 446-576	Mutation：N1024D, D1026E, T1027A, S1028T, V1034D, V1037I, Y1055W	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；292 K；30% PEG40, pH10.5, Microbatch under oil, temperature 292K	Resolution 2.48 Å R-free 0.276
3GJN Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-09	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 446–576（131 aa） Fragment：UNP residues 446-576	Mutation：N1024D, D1026E, T1027A, S1028T, V1034D, V1037I, Y1055W	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；292 K；30% PEG40, pH10.5, Microbatch under oil, temperature 292K	Resolution 2.48 Å R-free 0.276
3ZFK N-terminal truncated Nuclease Domain of Colicin E7 Deposited 2012-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 450–573（124 aa） Fragment：COLICIN E7 METALLONUCLEASE DOMAIN, RESIDUES 450-573	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1 M LITHIUM SULFATE, 50 MM SODIUM ACETATE PH 4.5, 25 % W/V PEG 400	Resolution 1.70 Å R-free 0.234
3ZFK N-terminal truncated Nuclease Domain of Colicin E7 Deposited 2012-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 450–573（124 aa） Fragment：COLICIN E7 METALLONUCLEASE DOMAIN, RESIDUES 450-573	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 4 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.1 M LITHIUM SULFATE, 50 MM SODIUM ACETATE PH 4.5, 25 % W/V PEG 400	Resolution 1.70 Å R-free 0.234
7CEI THE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITS INHIBITOR IM7 PROTEIN Deposited 1998-09-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–206（206 aa） Fragment：ENDONUCLEASE DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；15 MG/ML PROTEIN COMPLEX, 5 MM NA CITRATE, 0.25 M NH4 ACETATE, 10% PEG4000, PH 6.0 VAPOR DIFFUSION AGAINST 22.5% PEG4000	Resolution 2.30 Å R-free 0.270

16 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CEA7_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–141； UniProt 446–576 Author chain B； PDBConstruct 11–141； UniProt 446–576

Colicin-E7

Escherichia coli

UniProt P13479

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–86	Mutation：H545A	Colicin-E9 immunity protein × 1 （Q47112） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；292 K；30% PEG 400, 0.1 CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.20 Å R-free 0.277
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–86	Mutation：H545A	Colicin-E9 immunity protein × 1 （Q47112） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；292 K；30% PEG 400, 0.1 CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.20 Å R-free 0.277

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 3GKL	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	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
1E0H Inhibitor Protein Im9 bound to its partner E9 DNase Deposited 2000-03-28	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 A 1–86（86 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；295 K；Pressure 1 NMR sample composition 10% WATER/90% D2O	Resolution not provided
1EMV CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS) Deposited 2000-03-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Mutation：E41A	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
1IMP COLICIN E9 IMMUNITY PROTEIN IM9, NMR, 21 STRUCTURES Deposited 1996-05-30	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 A 1–86（86 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1IMQ COLICIN E9 IMMUNITY PROTEIN IM9, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-05-30	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 A 1–86（86 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2GYK Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A) Deposited 2006-05-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Mutation：D51A	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–86（86 aa）	Mutation：D51A	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Mutation：Y55A	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Mutation：Y54F	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Mutation：Y55F	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Mutation：V34A	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Mutation：D51A	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–86（86 aa）	Mutation：D51A	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
2K5X Chemical shift structure of COLICIN E9 DNASE domain with its cognate immunity protein IM9 Deposited 2008-07-01	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	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
3GJN Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–86（86 aa）	Mutation：H545A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；292 K；30% PEG40, pH10.5, Microbatch under oil, temperature 292K	Resolution 2.48 Å R-free 0.276
3GJN Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-09	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–86（86 aa）	Mutation：H545A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；292 K；30% PEG40, pH10.5, Microbatch under oil, temperature 292K	Resolution 2.48 Å R-free 0.276
3GJN Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–86（86 aa）	Mutation：H545A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.5；292 K；30% PEG40, pH10.5, Microbatch under oil, temperature 292K	Resolution 2.48 Å R-free 0.276
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–86（86 aa）	Not recorded	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–86（86 aa）	Not recorded	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–86（86 aa）	Not recorded	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–86（86 aa）	Not recorded	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

19 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMM9_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–86； UniProt 1–86 Author chain D； PDBConstruct 1–86； UniProt 1–86

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3gkl
Deposition date deposition_date	2009-03-11
Structure title title	Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins
Keywords keywords	;Protein-Protein complex, Structural Genomics, Israel Structural Proteomics Center, ISPC, Bacteriocin immunity, Plasmid, Antibiotic, Antimicrobial, Bacteriocin, Endonuclease, Hydrolase, Metal-binding, Nuclease, Zinc ;; HYDROLASE
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	24.09 Å
Radius of gyration Rg (electron density) rg_electron	23.15 Å
Forward intensity I(0) i0	38252900.00
Molecular weight molecular_weight	45683.0 kDa
Excluded volume excluded_volume	56400 Å³
Envelope volume envelope_volume	69005 Å³
Hydration-shell volume shell_volume	25182 Å³
Envelope diameter envelope_diameter	80.8 Å
Shell Rg shell_rg	30.00 Å
Envelope Rg envelope_rg	23.38 Å
Shape Rg shape_rg	23.14 Å
Total Rg total_rg	24.02 Å
Total atoms total_atoms	3213
Residues n_residues	404
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	80.7 Å
Rg (real space) rg_real	24.07 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	3.8250e+07
I(0) uncertainty (real space) i0_real_error	5.1440e+05
Rg (reciprocal space) rg_reciprocal	24.08 Å
I(0) (reciprocal space) i0_reciprocal	38250000.0000
Solution quality estimate total_estimate	0.8816
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.5 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.242
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10410000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.956

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Colicin-E9 immunity protein
Molecular weight formula_weight	16230.4 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	T20A, N24D, T27A, S28T, V34D, V37I, E41G, K57E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3223

MHHHHHHSMGKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHAEKPISQNGGVYDMDNISVVTPKRHIDIHRGK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Colicin-E7
Molecular weight formula_weight	9505.3 kDa
Mutation mutation	H545A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MELKHSISDYTEAEFLQLVATICDADATSEEELDKLITHFGEMTEHPSGSDLIYYPEEGDDDSPSGIVNTVKQWRAANGKSGFKQG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3gkla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.1 — HNH-motif

Domain ID domain_id	d3gklb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.1 — HNH-motif

Domain ID domain_id	d3gklc_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.2 — Colicin E immunity proteins
Family Family family	a.28.2.1 — Colicin E immunity proteins

Domain ID domain_id	d3gkld_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.2 — Colicin E immunity proteins
Family Family family	a.28.2.1 — Colicin E immunity proteins

CATH v4.4 (4 domains)

Domain ID domain_id	3gklA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
Homologous superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

Domain ID domain_id	3gklB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
Homologous superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

Domain ID domain_id	3gklC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	20 — Colicin E immunity protein

Domain ID domain_id	3gklD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	20 — Colicin E immunity protein

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8. Citations (1)

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Unit-cell length a length_a	54.161 Å
Unit-cell length b length_b	67.371 Å
Unit-cell length c length_c	123.231 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2414
R_work r_work	0.2396
R_free r_free	0.2768

fit	/app/data/saxs_computation/gk/3gkl/3gkl.fit
pddf	/app/data/pr_computation/gk/3gkl/3gkl.pr.out
profile	/app/data/saxs_computation/gk/3gkl/3gkl.dat

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins

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

Colicin-E9 immunity protein

State in the Current Structure

Other States of the Same Protein in the Database

Colicin-E7

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)