SAXSdb — 1ayi

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

COLICIN E IMMUNITY PROTEIN 7

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 1–87	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；USING THE HANGING DROP METHOD, PROTEIN (10MG/ML) WAS CRYSTALLISED BY MIXING AN EQUAL VOLUME OF PROTEIN WITH A SOLUTION CONTAINING 55% SATURATED DI-AMMONIUM PHOSPHATE AND 200MM TRIS PH7.2. THE DROP WAS EQUILIBRATED AGAINST A WELL CONTAINING 100% SATURATED DI-AMMONIUM PHOSPHATE AT ROOM TEMPERATURE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.247

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 1AYI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CEI STRUCTURE DETERMINATION OF THE COLICIN E7 IMMUNITY PROTEIN (IMME7) THAT BINDS SPECIFICALLY TO THE DNASE-TYPE COLICIN E7 AND INHIBITS ITS BACTERIOCIDAL ACTIVITY Deposited 1996-03-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.	Resolution 1.80 Å
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa）	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–87（87 aa）	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
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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa）	Mutation：D35Y,	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
1UNK STRUCTURE OF COLICIN E7 IMMUNITY PROTEIN Deposited 1996-06-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–87（87 aa） Chain B 1–87（87 aa） Chain C 1–87（87 aa） Chain D 1–87（87 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.251
1ZNV How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor Deposited 2005-05-12	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 1–87（87 aa）	Not recorded	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–87（87 aa）	Not recorded	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
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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–87（87 aa）	Mutation：D35Y, T51Q	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
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 A 1–87（87 aa） Chain C 1–87（87 aa）	Not recorded	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–87（87 aa）	Not recorded	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 A 1–87（87 aa） Chain C 1–87（87 aa）	Not recorded	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
2K0D NMR structure of a mutant colicin e7 immunity protein im7 with an extended helix III Deposited 2008-02-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 2–51（50 aa） Chain X 65–87（23 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 1 mM [U-99% 13C; U-99% 15N] potassium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 15N] potassium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] potassium phosphate, 100% D2O \| 100% D2O	Resolution not provided
4F37 Structure of the tethered N-terminus of Alzheimer's disease A peptide Deposited 2012-05-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–87（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Sodium malonate, 20% (w/v) PEG 3350, 0.1M Bis-tris propane pH 8.5, 0.2M 1-methylimidazolium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.57 Å R-free 0.269
4F37 Structure of the tethered N-terminus of Alzheimer's disease A peptide Deposited 2012-05-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 2–87（86 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Sodium malonate, 20% (w/v) PEG 3350, 0.1M Bis-tris propane pH 8.5, 0.2M 1-methylimidazolium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.57 Å R-free 0.269
5WNW Chaperone Spy bound to Im7 6-45 ensemble Deposited 2017-08-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 6–45（40 aa） Fragment：UNP residues 6-45	Not recorded	IMD IMIDAZOLE × 3 ZN ZINC ION × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；PEG 3000, imidazole, zinc acetate	Resolution 1.79 Å R-free 0.238
7CEI THE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITS INHIBITOR IM7 PROTEIN Deposited 1998-09-17	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 1–87（87 aa）	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

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

View Construct and Data Evidence

UniProt name	IMM7_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–87； UniProt 1–87

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	1ayi
Deposition date deposition_date	1997-11-04
Structure title title	COLICIN E7 IMMUNITY PROTEIN IM7
Keywords keywords	BACTERIOCIN, E COLICINS, PROTEIN-PROTEIN INTERACTIONS, DNASE INHIBITOR; BACTERIOCIN
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	13.95 Å
Radius of gyration Rg (electron density) rg_electron	12.39 Å
Forward intensity I(0) i0	1951100.00
Molecular weight molecular_weight	9454.0 kDa
Excluded volume excluded_volume	11816 Å³
Envelope volume envelope_volume	13483 Å³
Hydration-shell volume shell_volume	9580 Å³
Envelope diameter envelope_diameter	43.6 Å
Shell Rg shell_rg	17.63 Å
Envelope Rg envelope_rg	12.72 Å
Shape Rg shape_rg	12.37 Å
Total Rg total_rg	13.73 Å
Total atoms total_atoms	670
Residues n_residues	86
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	45.9 Å
Rg (real space) rg_real	13.87 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.9510e+06
I(0) uncertainty (real space) i0_real_error	2.2560e+04
Rg (reciprocal space) rg_reciprocal	13.87 Å
I(0) (reciprocal space) i0_reciprocal	1951000.0000
Solution quality estimate total_estimate	0.8757
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.139
Kurtosis Kurtosis kurtosis	-0.272
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	260100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ayia_
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 (1 domains)

Domain ID domain_id	1ayiA00
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	44.630 Å
Unit-cell length b length_b	50.677 Å
Unit-cell length c length_c	75.187 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1780
R_free r_free	0.2470

Description description	COLICIN E IMMUNITY PROTEIN 7
Molecular weight formula_weight	9907.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	704

COLICIN E7 IMMUNITY PROTEIN IM7

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

COLICIN E IMMUNITY PROTEIN 7

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

fit	/app/data/saxs_computation/ay/1ayi/1ayi.fit
pddf	/app/data/pr_computation/ay/1ayi/1ayi.pr.out
profile	/app/data/saxs_computation/ay/1ayi/1ayi.dat