1v13

CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)

Method: X-RAY DIFFRACTION D_max: 63.0 Å Quality: GOOD

▼

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

COLICIN E9

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 450–582 Chain B； UniProt 450–582	Mutation：YES	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.8；pH 5.80	Resolution 2.00 Å R-free 0.307

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 1V13	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BXI CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 Deposited 1998-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 449–582（134 aa） Fragment：DNASE DOMAIN, RESIDUES 450-581	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.3；24%(W/V)PEG 4K, 0.1MM SODIUM-ACETATE, PH5.3	Resolution 2.05 Å R-free 0.315
1EMV CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS) Deposited 2000-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% PEG 4000, 0.1M sodium acetate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.70 Å R-free 0.260
1FR2 CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANT IMMUNITY PROTEIN IM9(E41A) Deposited 2000-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN	Not recorded	PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% PEG 4000, 0.1M sodium acetate, , pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.232
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN	Not recorded	PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.80 Å R-free 0.222
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN	Not recorded	PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.80 Å R-free 0.222
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN	Not recorded	PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.80 Å R-free 0.222
1FSJ CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 450–582（133 aa） Fragment：C-TERMINAL DOMAIN OF E9 COLICIN	Not recorded	PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；285 K；30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.80 Å R-free 0.222
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.90 Å R-free 0.306
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.90 Å R-free 0.306
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.90 Å R-free 0.306
1V14 Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.90 Å R-free 0.306
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.40 Å R-free 0.329
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.40 Å R-free 0.329
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.40 Å R-free 0.329
1V15 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A) Deposited 2004-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain D 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 450-582	Mutation：YES	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 2.40 Å R-free 0.329
2GYK Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A) Deposited 2006-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.232
2GYK Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A) Deposited 2006-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 450–582（133 aa） Fragment：C-TERMINAL DOMAIN, DNASE DOMAIN	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.232
2GZE Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A) Deposited 2006-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：Colicin E9,C-terminal Domain,DNase Domain	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOUR DIFFUSSION,SITTING DROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.80 Å R-free 0.242
2GZF Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y54F) Deposited 2006-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：Colicin E9,C-terminal Domain,DNase Domain	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOUR DIFFUSSION,SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOUR DIFFUSSION,SITTING DROP, temperature 277K	Resolution 1.75 Å R-free 0.222
2GZG Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (Y55F) Deposited 2006-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.70 Å R-free 0.204
2GZI Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (V34A) Deposited 2006-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.70 Å R-free 0.256
2GZJ Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A) Deposited 2006-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.60 Å R-free 0.232
2GZJ Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A) Deposited 2006-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 450–582（133 aa） Fragment：COLICIN E9,C-TERMINAL DOMAIN,DNASE DOMAIN	Not recorded	ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP	Resolution 1.60 Å R-free 0.232
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2IVZ Structure of TolB in complex with a peptide of the colicin E9 T- domain Deposited 2006-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 32–47（16 aa） Fragment：T-DOMAIN, RESIDUES 32-47	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5	Resolution 2.00 Å R-free 0.222
2K5X Chemical shift structure of COLICIN E9 DNASE domain with its cognate immunity protein IM9 Deposited 2008-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：UNP residues 450-582	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；298 K	Resolution not provided
2VLN N75A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582	Mutation：YES	MLA MALONIC ACID × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.203
2VLO K97A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582	Mutation：YES	SO4 SULFATE ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.228
2VLP R54A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582	Mutation：YES	MLA MALONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions 2.9 M AMMONIUM SULPHATE AND 100 MM BIS-TRIS PH 5.5	Resolution 2.00 Å R-free 0.229
2VLQ F86A mutant of E9 DNase domain in complex with Im9 Deposited 2008-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa） Fragment：DNASE DOMAIN, RESIDUES 450-582	Mutation：YES	MLA MALONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions 2.9 M AMMONIUM SULPHATE AND 100 MM BIS-TRIS PH 5.5	Resolution 1.60 Å R-free 0.199
2WPT The crystal structure of Im2 in complex with colicin E9 DNase Deposited 2009-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 450–582（133 aa）	Mutation：YES	GOL GLYCEROL × 2 NO3 NITRATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；pH 6.8	Resolution 1.78 Å R-free 0.223
3O0E Crystal structure of OmpF in complex with colicin peptide OBS1 Deposited 2010-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 2–18（17 aa） Fragment：UNP Residues 2-18 Chain N 2–18（17 aa） Fragment：UNP Residues 2-18 Chain P 2–18（17 aa） Fragment：UNP Residues 2-18	Not recorded	BOG octyl beta-D-glucopyranoside × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2M Li2SO4, 0.1M sodium cacodylate, pH 6.5, sitting drop vapor diffusion, temperature 293K	Resolution 3.01 Å R-free 0.302
3O0E Crystal structure of OmpF in complex with colicin peptide OBS1 Deposited 2010-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 2–18（17 aa） Fragment：UNP Residues 2-18 Chain O 2–18（17 aa） Fragment：UNP Residues 2-18 Chain Q 2–18（17 aa） Fragment：UNP Residues 2-18	Not recorded	BOG octyl beta-D-glucopyranoside × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG 3350, 0.2M Li2SO4, 0.1M sodium cacodylate, pH 6.5, sitting drop vapor diffusion, temperature 293K	Resolution 3.01 Å R-free 0.302
4JML Crystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) complex. Deposited 2013-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 32–47（16 aa） Fragment：T-domain, Residues 32-47	Mutation：A33C	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；80mM calcium chloride, 24% PEG 5000MME, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.226
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–582（582 aa）	Mutation：Y324C, L447C, D448A, K449M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350	Resolution 3.20 Å R-free 0.271
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–582（582 aa）	Mutation：Y324C, L447C, D448A, K449M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350	Resolution 3.20 Å R-free 0.271
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–582（582 aa）	Mutation：Y324C, L447C, D448A, K449M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350	Resolution 3.20 Å R-free 0.271
5EW5 Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9 Deposited 2015-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–582（582 aa）	Mutation：Y324C, L447C, D448A, K449M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.3M sodium malonate, PEG3350	Resolution 3.20 Å R-free 0.271
7NST ColicinE9 partial translocation complex Deposited 2021-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–314（314 aa）	Mutation：A33C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane	Resolution 3.70 Å
7NSU ColicinE9 intact translocation complex Deposited 2021-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–582（582 aa）	Mutation：A33C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane	Resolution 4.70 Å

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

View Construct and Data Evidence

UniProt name	CEA9_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–134； UniProt 450–582 Author chain B； PDBConstruct 2–134； UniProt 450–582

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1v13
Deposition date deposition_date	2004-04-06
Structure title title	CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)
Keywords keywords	HOMING ENDONUCLEASES, COLICINS, BETA-BETA-ALPHA METAL ANTIBIOTIC, BACTERIOCIN, HYDROLASE, ENDONUCLEASE MOTIF, H-N-H MOTIF; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.38 Å
Radius of gyration Rg (electron density) rg_electron	18.63 Å
Forward intensity I(0) i0	14234500.00
Molecular weight molecular_weight	27224.0 kDa
Excluded volume excluded_volume	33657 Å³
Envelope volume envelope_volume	40180 Å³
Hydration-shell volume shell_volume	18300 Å³
Envelope diameter envelope_diameter	62.9 Å
Shell Rg shell_rg	24.59 Å
Envelope Rg envelope_rg	18.82 Å
Shape Rg shape_rg	18.60 Å
Total Rg total_rg	19.59 Å
Total atoms total_atoms	1916
Residues n_residues	246
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

▼

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

Maximum dimension Dmax dmax	63.0 Å
Rg (real space) rg_real	19.34 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	1.4230e+07
I(0) uncertainty (real space) i0_real_error	1.8040e+05
Rg (reciprocal space) rg_reciprocal	19.35 Å
I(0) (reciprocal space) i0_reciprocal	14230000.0000
Solution quality estimate total_estimate	0.8841
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.335
Kurtosis Kurtosis kurtosis	-0.308
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3912000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.990

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	COLICIN E9
Molecular weight formula_weight	15053.0 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	YES
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	2009

MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRGK

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 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1v13a_
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	d1v13b_
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

CATH v4.4 (2 domains)

Domain ID domain_id	1v13A00
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	1v13B00
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

▶

8. Citations (2)

▶

Unit-cell length a length_a	52.693 Å
Unit-cell length b length_b	61.441 Å
Unit-cell length c length_c	91.107 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	2.000 Å
Low-resolution limit resolution_low	50.640 Å
R factor r_factor	0.2340
R_work r_work	0.2300
R_free r_free	0.3070

fit	/app/data/saxs_computation/v1/1v13/1v13.fit
pddf	/app/data/pr_computation/v1/1v13/1v13.pr.out
profile	/app/data/saxs_computation/v1/1v13/1v13.dat