SAXSdb — 2no8

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–86	Not recorded	No other associated polymer	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

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 2NO8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WPT The crystal structure of Im2 in complex with colicin E9 DNase Deposited 2009-08-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
3U43 Crystal structure of the colicin E2 DNase-Im2 complex Deposited 2011-10-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	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
3U43 Crystal structure of the colicin E2 DNase-Im2 complex Deposited 2011-10-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–86（86 aa）	Not recorded	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 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMM2_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–86； UniProt 1–86

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	2no8
Deposition date deposition_date	2006-10-25
Structure title title	NMR Structure analysis of the colicin immuntiy protein IM2
Keywords keywords	4 helix bundle, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	12.76 Å
Radius of gyration Rg (electron density) rg_electron	12.27 Å
Forward intensity I(0) i0	5230870000.00
Molecular weight molecular_weight	591350.0 kDa
Excluded volume excluded_volume	727810 Å³
Envelope volume envelope_volume	21630 Å³
Hydration-shell volume shell_volume	12976 Å³
Envelope diameter envelope_diameter	44.5 Å
Shell Rg shell_rg	19.96 Å
Envelope Rg envelope_rg	14.28 Å
Shape Rg shape_rg	12.25 Å
Total Rg total_rg	12.40 Å
Total atoms total_atoms	81180
Residues n_residues	5100
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	37.4 Å
Rg (real space) rg_real	12.66 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	5.2310e+09
I(0) uncertainty (real space) i0_real_error	5.3480e+07
Rg (reciprocal space) rg_reciprocal	12.67 Å
I(0) (reciprocal space) i0_reciprocal	5231000000.0000
Solution quality estimate total_estimate	0.8337
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.0 Å
Skewness Skewness skewness	0.029
Kurtosis Kurtosis kurtosis	-0.425
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	111100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2no8a_
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	2no8A00
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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Description description	Colicin-E2 immunity protein
Molecular weight formula_weight	10011.0 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	81180

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

fit	/app/data/saxs_computation/no/2no8/2no8.fit
pddf	/app/data/pr_computation/no/2no8/2no8.pr.out
profile	/app/data/saxs_computation/no/2no8/2no8.dat

NMR Structure analysis of the colicin immuntiy protein IM2

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

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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)