SAXSdb — 4udm

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

COLICIN-E3 IMMUNITY PROTEIN

ESCHERICHIA COLI BL21(DE3)

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 1–85	Not recorded	COLICIN-E3 × 1 （P00646） CA CALCIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；0.1M BIS-TRIS PH 6.5, 50MM CACL2,30%PEG550MME	Resolution 2.96 Å R-free 0.214

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 4UDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E44 ribonuclease domain of colicin E3 in complex with its immunity protein Deposited 2000-06-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–85（85 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.1 M NA CITRATE PH 5.6, 20% ISOPROPANOL, 10% PEG 4000	Resolution 2.40 Å R-free 0.228
1JCH Crystal Structure of Colicin E3 in Complex with its Immunity Protein Deposited 2001-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–84（84 aa） Chain D 1–84（84 aa）	Not recorded	CIT CITRIC ACID × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.02 Å R-free 0.283
1JCH Crystal Structure of Colicin E3 in Complex with its Immunity Protein Deposited 2001-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–84（84 aa）	Not recorded	CIT CITRIC ACID × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.02 Å R-free 0.283
1JCH Crystal Structure of Colicin E3 in Complex with its Immunity Protein Deposited 2001-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–84（84 aa）	Not recorded	CIT CITRIC ACID × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.02 Å R-free 0.283
2B5U Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein Deposited 2005-09-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–84（84 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.295
2B5U Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein Deposited 2005-09-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–84（84 aa）	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.295
3EIP CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE Deposited 1999-03-29	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 2–85（84 aa） Chain B 2–85（84 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；2.0 M AMMONIUM SULFATE, 0.1 M MES BUFFER, PH 6.0, pH 6.00	Resolution 1.80 Å R-free 0.265

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMM3_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 1–85

COLICIN-E3

ESCHERICHIA COLI BL21(DE3)

UniProt P00646

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 456–551	Fragment：RIBONUCLEASE DOMAIN, UNP RESIDUES 456-551 Mutation：YES	COLICIN-E3 IMMUNITY PROTEIN × 1 （P02984） CA CALCIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；0.1M BIS-TRIS PH 6.5, 50MM CACL2,30%PEG550MME	Resolution 2.96 Å R-free 0.214

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 4UDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E44 ribonuclease domain of colicin E3 in complex with its immunity protein Deposited 2000-06-28	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 456–551（96 aa） Fragment：RIBONUCLEASE DOMAIN RESIDUES 456-551	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；0.1 M NA CITRATE PH 5.6, 20% ISOPROPANOL, 10% PEG 4000	Resolution 2.40 Å R-free 0.228
1JCH Crystal Structure of Colicin E3 in Complex with its Immunity Protein Deposited 2001-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–551（551 aa） Chain C 1–551（551 aa）	Not recorded	CIT CITRIC ACID × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.02 Å R-free 0.283
1JCH Crystal Structure of Colicin E3 in Complex with its Immunity Protein Deposited 2001-06-09	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 A 1–551（551 aa）	Not recorded	CIT CITRIC ACID × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.02 Å R-free 0.283
1JCH Crystal Structure of Colicin E3 in Complex with its Immunity Protein Deposited 2001-06-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–551（551 aa）	Not recorded	CIT CITRIC ACID × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.02 Å R-free 0.283
1UJW Structure of the complex between BtuB and Colicin E3 Receptor binding domain Deposited 2003-08-12	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 314–448（135 aa） Fragment：R-domain(residues 314-448)	Not recorded	GP1 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose × 2 LIM 3-OXO-PENTADECANOIC ACID × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 7 AAE ACETOACETIC ACID × 1 GOL GLYCEROL × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.75 Å R-free 0.293
2B5U Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein Deposited 2005-09-29	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 A 1–551（551 aa）	Mutation：V206C	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.295
2B5U Crystal Structure Of Colicin E3 V206C Mutant In Complex With Its Immunity Protein Deposited 2005-09-29	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 C 1–551（551 aa）	Mutation：V206C	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；Sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.295
4V5K Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome Deposited 2010-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 52 PDB declaration: 58-meric	Chain AY 455–551（97 aa） Fragment：RESIDUES 455-551	Mutation：YES	MG MAGNESIUM ION × 1164 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.18；AS STATED IN STRUCTURE OF THE 70S RIBOSOME COMPLEXED WITH MRNA AND TRNA. (2006) SCIENCE 313: 1935, PH 7.18	Resolution 3.20 Å R-free 0.270
4V5K Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome Deposited 2010-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 52 PDB declaration: 58-meric	Chain CY 455–551（97 aa） Fragment：RESIDUES 455-551	Mutation：YES	MG MAGNESIUM ION × 1170 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.18；AS STATED IN STRUCTURE OF THE 70S RIBOSOME COMPLEXED WITH MRNA AND TRNA. (2006) SCIENCE 313: 1935, PH 7.18	Resolution 3.20 Å R-free 0.270

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CEA3_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–96； UniProt 456–551

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	4udm
Deposition date deposition_date	2014-12-10
Structure title title	Crystal structure of Im3 in complex with Y52A mutant of E3RNase
Keywords keywords	;TRANSLATION, ANTIBIOTIC, ANTIMICROBIAL, BACTERIOCIN, BACTERIOCIN IMMUNITY, ENDONUCLEASE, HYDROLASE, INHIBITION, NUCLEASE, PROTEIN-PROTEIN INTERACTIONS, RIBONUCLEASE, RIBOSOME INACTIVATION, TOXIN ;; TRANSLATION
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	17.15 Å
Radius of gyration Rg (electron density) rg_electron	16.06 Å
Forward intensity I(0) i0	8205580.00
Molecular weight molecular_weight	20619.0 kDa
Excluded volume excluded_volume	25554 Å³
Envelope volume envelope_volume	29507 Å³
Hydration-shell volume shell_volume	15466 Å³
Envelope diameter envelope_diameter	51.6 Å
Shell Rg shell_rg	21.86 Å
Envelope Rg envelope_rg	16.22 Å
Shape Rg shape_rg	16.02 Å
Total Rg total_rg	17.17 Å
Total atoms total_atoms	1455
Residues n_residues	180
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	52.7 Å
Rg (real space) rg_real	17.04 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	8.2060e+06
I(0) uncertainty (real space) i0_real_error	9.1080e+04
Rg (reciprocal space) rg_reciprocal	17.06 Å
I(0) (reciprocal space) i0_reciprocal	8206000.0000
Solution quality estimate total_estimate	0.9037
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.481
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1829000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.994

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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-E3 IMMUNITY PROTEIN
Molecular weight formula_weight	9910.8 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	1490

MGLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW

来源 Source

来源生物 organism	ESCHERICHIA COLI BL21(DE3)
NCBI Class编号 ncbi_taxonomy_id	469008
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	COLICIN-E3
Molecular weight formula_weight	10720.0 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIAEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL

来源 Source

来源生物 organism	ESCHERICHIA COLI BL21(DE3)
NCBI Class编号 ncbi_taxonomy_id	469008
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	4

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4udma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.2 — Colicin E3 immunity protein
Family Family family	d.26.2.1 — Colicin E3 immunity protein

Domain ID domain_id	d4udmb_
Class class	b — All beta proteins
Fold Fold fold	b.101 — Ribonuclease domain of colicin E3
Superfamily Superfamily superfamily	b.101.1 — Ribonuclease domain of colicin E3
Family Family family	b.101.1.1 — Ribonuclease domain of colicin E3

CATH v4.4 (2 domains)

Domain ID domain_id	4udmA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	20 — Cloacin immunity protein

Domain ID domain_id	4udmB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	380 — Ribonuclease domain of colicin e3 (Residues 456-551)
Homologous superfamily homologous superfamily	10 — Colicin E3-like ribonuclease domain

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8. Citations (1)

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Unit-cell length a length_a	92.854 Å
Unit-cell length b length_b	92.854 Å
Unit-cell length c length_c	76.942 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.960 Å
Low-resolution limit resolution_low	38.470 Å
R factor r_factor	0.1857
R_work r_work	0.1842
R_free r_free	0.2138

fit	/app/data/saxs_computation/ud/4udm/4udm.fit
pddf	/app/data/pr_computation/ud/4udm/4udm.pr.out
profile	/app/data/saxs_computation/ud/4udm/4udm.dat

Crystal structure of Im3 in complex with Y52A mutant of E3RNase

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

COLICIN-E3 IMMUNITY PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

COLICIN-E3

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)