SAXSdb — 1z9b

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

Translation initiation factor IF-2

Geobacillus stearothermophilus

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 515–635	Fragment：Bst IF2-C1 subdomain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.4；307.4 K；Ionic strength (raw mmCIF value) 200 mM KCl；Pressure ambient NMR sample composition：0.5 mM Bst IF2-C1 U-15N & U-13C; 20 mM KPi; 200 mM KCl, protease inhibitor mix, NaN3 \| 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 1Z9B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D1N SOLUTION STRUCTURE OF THE FMET-TRNAFMET BINDING DOMAIN OF BECILLUS STEAROTHERMOPHILLUS TRANSLATION INITIATION FACTOR IF2 Deposited 1999-09-20	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 643–741（99 aa） Fragment：C2 TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2LKC Free B.st IF2-G2 Deposited 2011-10-10	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 241–414（174 aa） Fragment：G-domain region residues 241-414	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；315 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 0.4-0.9 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LKD IF2-G2 GDP complex Deposited 2011-10-10	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 241–414（174 aa） Fragment：G-domain region residues 241-414	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1	SOLUTION NMR NMR measurement conditions pH 6.5；315 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 0.4-0.9 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NBG Structure of the Geobacillus stearothermophilus IF2 G3-subdomain Deposited 2016-02-11	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 394–514（121 aa） Fragment：residues 394-514	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.15 mM [U-100% 13C; U-100% 15N] IF2-G3, 50 mM sodium phosphate, 100 mM potassium chloride, 2 % glycerol, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	IF2_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–135； UniProt 515–635

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	1z9b
Deposition date deposition_date	2005-04-01
Structure title title	Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2
Keywords keywords	protein synthesis translation intiation IF2 fMet-tRNA NMR structure, TRANSLATION; TRANSLATION
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	29.68 Å
Radius of gyration Rg (electron density) rg_electron	29.22 Å
Forward intensity I(0) i0	1253710000.00
Molecular weight molecular_weight	295180.0 kDa
Excluded volume excluded_volume	369930 Å³
Envelope volume envelope_volume	216730 Å³
Hydration-shell volume shell_volume	46527 Å³
Envelope diameter envelope_diameter	138.3 Å
Shell Rg shell_rg	42.57 Å
Envelope Rg envelope_rg	42.13 Å
Shape Rg shape_rg	29.24 Å
Total Rg total_rg	29.54 Å
Total atoms total_atoms	41760
Residues n_residues	2700
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	125.0 Å
Rg (real space) rg_real	30.45 Å
Rg uncertainty (real space) rg_real_error	2.41 Å
I(0) (real space) i0_real	1.2540e+09
I(0) uncertainty (real space) i0_real_error	2.3750e+07
Rg (reciprocal space) rg_reciprocal	30.12 Å
I(0) (reciprocal space) i0_reciprocal	1253000000.0000
Solution quality estimate total_estimate	0.6251
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.682
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	566400.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.040; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.001; Smooth: 0.999

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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	1z9bA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10050 — Translation initiation factor IF- 2, domain 3

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8. Citations (1)

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Description description	Translation initiation factor IF-2
Molecular weight formula_weight	14815.9 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	41760

来源生物 organism	Geobacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/z9/1z9b/1z9b.fit
pddf	/app/data/pr_computation/z9/1z9b/1z9b.pr.out
profile	/app/data/saxs_computation/z9/1z9b/1z9b.dat

Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2

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

Translation initiation factor IF-2

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)