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2nbg

Structure of the Geobacillus stearothermophilus IF2 G3-subdomain

Method: SOLUTION NMR Dmax: 49.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Translation initiation factor IF-2

Geobacillus stearothermophilus

UniProt P04766

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 394–514 Fragment：residues 394-514 No other associated polymer 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

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 2NBG 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
1Z9B Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2 Deposited 2005-04-01 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 515–635（121 aa） Fragment：Bst IF2-C1 subdomain
Not recorded No recorded non-water small molecule 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
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

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

View Construct and Data Evidence
UniProt name IF2_GEOSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–125； UniProt 394–514

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2nbg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2nbg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2nbg
Deposition date deposition_date2016-02-11
Structure title titleStructure of the Geobacillus stearothermophilus IF2 G3-subdomain
Keywords keywordsribosome, translation initiation, TRANSLATION; TRANSLATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.28 Å
Radius of gyration Rg (electron density) rg_electron17.91 Å
Forward intensity I(0) i01120010000.00
Molecular weight molecular_weight272600.0 kDa
Excluded volume excluded_volume339170 ų
Envelope volume envelope_volume104150 ų
Hydration-shell volume shell_volume32387 ų
Envelope diameter envelope_diameter104.3 Å
Shell Rg shell_rg34.22 Å
Envelope Rg envelope_rg27.53 Å
Shape Rg shape_rg17.86 Å
Total Rg total_rg18.62 Å
Total atoms total_atoms38740
Residues n_residues2500
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax49.8 Å
Rg (real space) rg_real17.18 Å
Rg uncertainty (real space) rg_real_error0.08 Å
I(0) (real space) i0_real1.0660e+09
I(0) uncertainty (real space) i0_real_error1.0180e+07
Rg (reciprocal space) rg_reciprocal18.48 Å
I(0) (reciprocal space) i0_reciprocal1120000000.0000
Solution quality estimate total_estimate0.6774
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary18.2 Å
Skewness Skewness skewness0.419
Kurtosis Kurtosis kurtosis-0.394
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha4.5300
Highest regularization parameter α highest_alpha1060000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.007; Oscil: 0.954; Stabil: 0.984; Sysdev: 0.000; Positv: 1.000; Valcen: 0.992; 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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8. Citations (1)

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9. Files and Curves (10)