SAXSdb — 1e44

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

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 1–85	Not recorded	COLICIN E3 × 1 （P00646） 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

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 1E44	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
4UDM Crystal structure of Im3 in complex with Y52A mutant of E3RNase Deposited 2014-12-10	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	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

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

View Construct and Data Evidence

UniProt name	IMM3_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–85； UniProt 1–85

COLICIN E3

ESCHERICHIA COLI

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 RESIDUES 456-551	IMMUNITY PROTEIN × 1 （P02984） 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

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 1E44	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 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 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
4UDM Crystal structure of Im3 in complex with Y52A mutant of E3RNase Deposited 2014-12-10	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, UNP RESIDUES 456-551	Mutation：YES	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
4V5K Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome Deposited 2010-05-29	Different construct Different mutation/modification 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 mutation/modification 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_ECOLI
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	1e44
Deposition date deposition_date	2000-06-28
Structure title title	ribonuclease domain of colicin E3 in complex with its immunity protein
Keywords keywords	RIBONUCLEASE, INHIBITION, PROTEIN-PROTEIN INTERACTIONS, RIBOSOME INACTIVATION, TOXIN; RIBONUCLEASE
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	17.08 Å
Radius of gyration Rg (electron density) rg_electron	15.99 Å
Forward intensity I(0) i0	8132930.00
Molecular weight molecular_weight	20618.0 kDa
Excluded volume excluded_volume	25586 Å³
Envelope volume envelope_volume	29116 Å³
Hydration-shell volume shell_volume	15322 Å³
Envelope diameter envelope_diameter	51.9 Å
Shell Rg shell_rg	21.85 Å
Envelope Rg envelope_rg	16.18 Å
Shape Rg shape_rg	15.95 Å
Total Rg total_rg	17.07 Å
Total atoms total_atoms	1462
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	53.0 Å
Rg (real space) rg_real	16.97 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	8.1330e+06
I(0) uncertainty (real space) i0_real_error	8.5210e+04
Rg (reciprocal space) rg_reciprocal	16.98 Å
I(0) (reciprocal space) i0_reciprocal	8133000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.130
Kurtosis Kurtosis kurtosis	-0.487
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1900000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	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	1633

MGLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW

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 E3
Molecular weight formula_weight	10812.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIYEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1e44a_
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	d1e44b_
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	1e44A00
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	1e44B00
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	93.700 Å
Unit-cell length b length_b	93.700 Å
Unit-cell length c length_c	76.170 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	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2280

fit	/app/data/saxs_computation/e4/1e44/1e44.fit
pddf	/app/data/pr_computation/e4/1e44/1e44.pr.out
profile	/app/data/saxs_computation/e4/1e44/1e44.dat

ribonuclease domain of colicin E3 in complex with its immunity protein

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

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 (4)

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 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)