SAXSdb — 1d1n

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

INITIATION FACTOR 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 643–741	Fragment：C2 TERMINAL DOMAIN	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	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 1D1N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
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 1–99； UniProt 643–741

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	1d1n
Deposition date deposition_date	1999-09-20
Structure title title	SOLUTION STRUCTURE OF THE FMET-TRNAFMET BINDING DOMAIN OF BECILLUS STEAROTHERMOPHILLUS TRANSLATION INITIATION FACTOR IF2
Keywords keywords	BETA-BARREL, GENE REGULATION; GENE REGULATION
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	13.01 Å
Radius of gyration Rg (electron density) rg_electron	12.97 Å
Forward intensity I(0) i0	692779000.00
Molecular weight molecular_weight	223220.0 kDa
Excluded volume excluded_volume	279840 Å³
Envelope volume envelope_volume	24661 Å³
Hydration-shell volume shell_volume	13798 Å³
Envelope diameter envelope_diameter	52.7 Å
Shell Rg shell_rg	21.07 Å
Envelope Rg envelope_rg	15.60 Å
Shape Rg shape_rg	12.94 Å
Total Rg total_rg	13.22 Å
Total atoms total_atoms	31620
Residues n_residues	1980
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	47.4 Å
Rg (real space) rg_real	12.95 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	6.9280e+08
I(0) uncertainty (real space) i0_real_error	7.0600e+06
Rg (reciprocal space) rg_reciprocal	12.96 Å
I(0) (reciprocal space) i0_reciprocal	692800000.0000
Solution quality estimate total_estimate	0.8224
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.248
Kurtosis Kurtosis kurtosis	-0.135
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	423800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.571; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d1na_
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.1 — Elongation factors

CATH v4.4 (1 domains)

Domain ID domain_id	1d1nA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	INITIATION FACTOR 2
Molecular weight formula_weight	11210.7 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	31620

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

SOLUTION STRUCTURE OF THE FMET-TRNAFMET BINDING DOMAIN OF BECILLUS STEAROTHERMOPHILLUS TRANSLATION INITIATION FACTOR IF2

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

INITIATION FACTOR 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

Unit cell Unit Cell

Symmetry Symmetry

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)

fit	/app/data/saxs_computation/d1/1d1n/1d1n.fit
pddf	/app/data/pr_computation/d1/1d1n/1d1n.pr.out
profile	/app/data/saxs_computation/d1/1d1n/1d1n.dat