SAXSdb — 3u43

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

Colicin-E2 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 1–86	Not recorded	Colicin-E2 × 1 （P04419） ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M MMT, 27% PEG1500, pH 7.0, vapor diffusion, sitting drop, temperature 293K	Resolution 1.72 Å R-free 0.203
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–86	Not recorded	Colicin-E2 × 1 （P04419） ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M MMT, 27% PEG1500, pH 7.0, vapor diffusion, sitting drop, temperature 293K	Resolution 1.72 Å R-free 0.203

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 3U43	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NO8 NMR Structure analysis of the colicin immuntiy protein IM2 Deposited 2006-10-25	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；298 K；Pressure 1 NMR sample composition 50mM phosphate buffer NA, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
2WPT The crystal structure of Im2 in complex with colicin E9 DNase Deposited 2009-08-10	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：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

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

View Construct and Data Evidence

UniProt name	IMM2_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–86； UniProt 1–86

Colicin-E2

Escherichia coli

UniProt P04419

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 B； UniProt 449–581	Fragment：DNase domain (UNP residues 449-581)	Colicin-E2 immunity protein × 1 （P04482） ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M MMT, 27% PEG1500, pH 7.0, vapor diffusion, sitting drop, temperature 293K	Resolution 1.72 Å R-free 0.203
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 449–581	Fragment：DNase domain (UNP residues 449-581)	Colicin-E2 immunity protein × 1 （P04482） ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M MMT, 27% PEG1500, pH 7.0, vapor diffusion, sitting drop, temperature 293K	Resolution 1.72 Å R-free 0.203

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 3U43	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YSU Structure of the complex between BtuB and Colicin E2 receptor binding domain Deposited 2007-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 313–447（135 aa） Fragment：R-DOMAIN(RESIDUES 313-447)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.315

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CEA2_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–134； UniProt 449–581

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	3u43
Deposition date deposition_date	2011-10-07
Structure title title	Crystal structure of the colicin E2 DNase-Im2 complex
Keywords keywords	protein-protein complex, DNase, high affinity, PROTEIN BINDING; PROTEIN BINDING
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	21.08 Å
Radius of gyration Rg (electron density) rg_electron	20.31 Å
Forward intensity I(0) i0	13152900.00
Molecular weight molecular_weight	25888.0 kDa
Excluded volume excluded_volume	31880 Å³
Envelope volume envelope_volume	39087 Å³
Hydration-shell volume shell_volume	17193 Å³
Envelope diameter envelope_diameter	84.1 Å
Shell Rg shell_rg	25.25 Å
Envelope Rg envelope_rg	21.24 Å
Shape Rg shape_rg	20.34 Å
Total Rg total_rg	20.91 Å
Total atoms total_atoms	1825
Residues n_residues	224
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	82.7 Å
Rg (real space) rg_real	21.32 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	1.3150e+07
I(0) uncertainty (real space) i0_real_error	1.7940e+05
Rg (reciprocal space) rg_reciprocal	21.27 Å
I(0) (reciprocal space) i0_reciprocal	13150000.0000
Solution quality estimate total_estimate	0.7470
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.720
Kurtosis Kurtosis kurtosis	0.399
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2394000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.396; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.521; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Colicin-E2 immunity protein
Molecular weight formula_weight	11082.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2206

MELKHSISDYTEAEFLEFVKKICRAEGATEEDDNKLVREFERLTEHPDGSDLIYYPRDDREDSPEGIVKEIKEWRAANGKSGFKQGLEHHHHHH

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-E2
Molecular weight formula_weight	15367.4 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKNFDDFRKKFWEEVSKDPDLSKQFKGSNKTNIQKGKAPFARKKDQVGGRERFELHHDKPISQDGGVYDMNNIRVTTPKRHIDIHRGK

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	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	319

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3u43a1
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	d3u43a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3u43b_
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	3u43A00
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	3u43B00
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	121.814 Å
Unit-cell length b length_b	53.277 Å
Unit-cell length c length_c	32.785 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	48.810 Å
R factor r_factor	0.1638
R_work r_work	0.1616
R_free r_free	0.2025

fit	/app/data/saxs_computation/u4/3u43/3u43.fit
pddf	/app/data/pr_computation/u4/3u43/3u43.pr.out
profile	/app/data/saxs_computation/u4/3u43/3u43.dat

Crystal structure of the colicin E2 DNase-Im2 complex

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

Colicin-E2 immunity protein

State in the Current Structure

Other States of the Same Protein in the Database

Colicin-E2

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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)