SAXSdb — 3eip

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

PROTEIN (COLICIN E3 IMMUNITY PROTEIN)

Escherichia coli str. K12 substr.

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 2–85 Chain B； UniProt 2–85	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

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 3EIP	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–85（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 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 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 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 mutation/modification Different oligomeric state 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 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 1–84（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 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 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
4UDM Crystal structure of Im3 in complex with Y52A mutant of E3RNase Deposited 2014-12-10	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 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 1–84； UniProt 2–85 Author chain B； PDBConstruct 1–84； UniProt 2–85

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	3eip
Deposition date deposition_date	1999-03-29
Structure title title	CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE
Keywords keywords	RIBONUCLEASE INHIBITOR, COLICIN, IMMUNE SYSTEM; IMMUNE SYSTEM
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	17.43 Å
Radius of gyration Rg (electron density) rg_electron	16.36 Å
Forward intensity I(0) i0	7316360.00
Molecular weight molecular_weight	19584.0 kDa
Excluded volume excluded_volume	24236 Å³
Envelope volume envelope_volume	28343 Å³
Hydration-shell volume shell_volume	14743 Å³
Envelope diameter envelope_diameter	49.8 Å
Shell Rg shell_rg	21.96 Å
Envelope Rg envelope_rg	16.37 Å
Shape Rg shape_rg	16.34 Å
Total Rg total_rg	17.36 Å
Total atoms total_atoms	1387
Residues n_residues	168
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	53.1 Å
Rg (real space) rg_real	17.32 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	7.3160e+06
I(0) uncertainty (real space) i0_real_error	8.1570e+04
Rg (reciprocal space) rg_reciprocal	17.33 Å
I(0) (reciprocal space) i0_reciprocal	7316000.0000
Solution quality estimate total_estimate	0.8291
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.107
Kurtosis Kurtosis kurtosis	-0.579
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1686000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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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	PROTEIN (COLICIN E3 IMMUNITY PROTEIN)
Molecular weight formula_weight	9779.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1505

GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW

来源 Source

来源生物 organism	Escherichia coli str. K12 substr.
NCBI Class编号 ncbi_taxonomy_id	316407
宿主生物 host_organism	Escherichia coli str. K12 substr. W3110

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	118

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3eipa_
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	d3eipb_
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

CATH v4.4 (2 domains)

Domain ID domain_id	3eipA00
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	3eipB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	20 — Cloacin immunity protein

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8. Citations (1)

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Unit-cell length a length_a	80.070 Å
Unit-cell length b length_b	53.720 Å
Unit-cell length c length_c	36.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	44.600 Å
R factor r_factor	—
R_work r_work	0.2178
R_free r_free	0.2651

fit	/app/data/saxs_computation/ei/3eip/3eip.fit
pddf	/app/data/pr_computation/ei/3eip/3eip.pr.out
profile	/app/data/saxs_computation/ei/3eip/3eip.dat

CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A RIBOSOME-INACTIVATING RNASE

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

PROTEIN (COLICIN E3 IMMUNITY PROTEIN)

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