SAXSdb — 3fbd

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

Colicin-E7

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 445–576	Fragment：NUCLEASE DOMAIN Mutation：D493Q	5'-D(DGPDGPDAPDAPDTPDTPDCPDGPDAPDTPDCPDGPDAPDAPDTPDTPDCPDC)-3' × 2	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
2	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain D； UniProt 445–576	Fragment：NUCLEASE DOMAIN Mutation：D493Q	5'-D(DGPDGPDAPDAPDTPDTPDCPDGPDAPDTPDCPDGPDAPDAPDTPDTPDCPDC)-3' × 2	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

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 3FBD	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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 ligand/ion 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 ligand/ion 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
3GJN Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-09	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 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 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 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
3GKL Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-11	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 A 446–576（131 aa） Fragment：UNP residues 446-576	Mutation：T20A, N24D, T27A, S28T, V34D, V37I, E41G, K57E	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
3GKL Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins Deposited 2009-03-11	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 B 446–576（131 aa） Fragment：UNP residues 446-576	Mutation：T20A, N24D, T27A, S28T, V34D, V37I, E41G, K57E	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
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 oligomeric state Different ligand/ion 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 1–132； UniProt 445–576 Author chain D； PDBConstruct 1–132； UniProt 445–576

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	3fbd
Deposition date deposition_date	2008-11-19
Structure title title	Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA
Keywords keywords	;Computational redesign, Protein engineering, Protein-nucleic acid interactions, DNase, DNA hydrolysis., Antibiotic, Antimicrobial, Bacteriocin, Endonuclease, Hydrolase, Metal-binding, Nuclease, Plasmid, Zinc, HYDROLASE-DNA COMPLEX ;; HYDROLASE/DNA
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	39.44 Å
Radius of gyration Rg (electron density) rg_electron	42.05 Å
Forward intensity I(0) i0	69215900.00
Molecular weight molecular_weight	52256.0 kDa
Excluded volume excluded_volume	58878 Å³
Envelope volume envelope_volume	90614 Å³
Hydration-shell volume shell_volume	19528 Å³
Envelope diameter envelope_diameter	130.1 Å
Shell Rg shell_rg	42.79 Å
Envelope Rg envelope_rg	40.70 Å
Shape Rg shape_rg	42.12 Å
Total Rg total_rg	41.90 Å
Total atoms total_atoms	3592
Residues n_residues	335
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	121.0 Å
Rg (real space) rg_real	39.75 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	6.8340e+07
I(0) uncertainty (real space) i0_real_error	1.0320e+06
Rg (reciprocal space) rg_reciprocal	39.78 Å
I(0) (reciprocal space) i0_reciprocal	69180000.0000
Solution quality estimate total_estimate	0.4344
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.450
Kurtosis Kurtosis kurtosis	-0.955
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	1.5840
Highest regularization parameter α highest_alpha	2295000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.292; Stabil: 0.895; Sysdev: 0.000; Positv: 1.000; Valcen: 0.080; Smooth: 0.006

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Colicin-E7
Molecular weight formula_weight	15162.2 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	D493Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	3663

SKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFQDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK

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	5'-D(DGPDGPDAPDAPDTPDTPDCPDGPDAPDTPDCPDGPDAPDAPDTPDTPDCPDC)-3'
Molecular weight formula_weight	5515.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C,E,F

GGAATTCGATCGAATTCC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3fbda_
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	d3fbdd_
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	3fbdA00
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	3fbdD00
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

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8. Citations (1)

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Unit-cell length a length_a	60.587 Å
Unit-cell length b length_b	49.423 Å
Unit-cell length c length_c	92.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	27.200 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2640

fit	/app/data/saxs_computation/fb/3fbd/3fbd.fit
pddf	/app/data/pr_computation/fb/3fbd/3fbd.pr.out
profile	/app/data/saxs_computation/fb/3fbd/3fbd.dat

Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA

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

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)