SAXSdb — 1bkb

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

TRANSLATION INITIATION FACTOR 5A

Pyrobaculum aerophilum

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–136	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；281 K；PROTEIN WAS CRYSTALLIZED AT 8 DEGREES IN 50MM HEPES PH 7.5, 6-8% PEG 4000, 5MM BETA- MERCAPTOETHANOL, temperature 281K	Resolution 1.75 Å R-free 0.236

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	IF5A_PYRAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136

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	1bkb
Deposition date deposition_date	1998-07-05
Structure title title	INITIATION FACTOR 5A FROM ARCHEBACTERIUM PYROBACULUM AEROPHILUM
Keywords keywords	TRANSLATION INITIATION FACTOR, TRANSLATION; TRANSLATION
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	18.58 Å
Radius of gyration Rg (electron density) rg_electron	17.78 Å
Forward intensity I(0) i0	4418510.00
Molecular weight molecular_weight	15316.0 kDa
Excluded volume excluded_volume	19274 Å³
Envelope volume envelope_volume	23006 Å³
Hydration-shell volume shell_volume	12121 Å³
Envelope diameter envelope_diameter	70.9 Å
Shell Rg shell_rg	21.83 Å
Envelope Rg envelope_rg	18.18 Å
Shape Rg shape_rg	17.74 Å
Total Rg total_rg	18.67 Å
Total atoms total_atoms	1062
Residues n_residues	132
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	71.5 Å
Rg (real space) rg_real	18.76 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	4.4190e+06
I(0) uncertainty (real space) i0_real_error	5.7960e+04
Rg (reciprocal space) rg_reciprocal	18.74 Å
I(0) (reciprocal space) i0_reciprocal	4418000.0000
Solution quality estimate total_estimate	0.7672
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.618
Kurtosis Kurtosis kurtosis	0.141
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	957300.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.502; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.956

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bkba1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.5 — Translation proteins SH3-like domain
Family Family family	b.34.5.2 — eIF5a N-terminal domain-like

Domain ID domain_id	d1bkba2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	1bkbA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1bkbA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	114.130 Å
Unit-cell length b length_b	114.130 Å
Unit-cell length c length_c	32.590 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	8

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2360

Description description	TRANSLATION INITIATION FACTOR 5A
Molecular weight formula_weight	15334.2 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1234

INITIATION FACTOR 5A FROM ARCHEBACTERIUM PYROBACULUM AEROPHILUM

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

TRANSLATION INITIATION FACTOR 5A

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pyrobaculum aerophilum
NCBI Class编号 ncbi_taxonomy_id	13773
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	143

fit	/app/data/saxs_computation/bk/1bkb/1bkb.fit
pddf	/app/data/pr_computation/bk/1bkb/1bkb.pr.out
profile	/app/data/saxs_computation/bk/1bkb/1bkb.dat