SAXSdb — 1b4b

▼

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

ARGININE REPRESSOR

OrganismNot specified

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 79–149 Chain B； UniProt 79–149 Chain C； UniProt 79–149	Fragment：OLIGOMERIZATION DOMAIN, L-ARGININE BINDING DOMAIN	ARG ARGININE × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.266

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 1B4B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4A STRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS Deposited 1998-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–149（148 aa） Chain B 2–149（148 aa） Chain C 2–149（148 aa） Chain D 2–149（148 aa） Chain E 2–149（148 aa） Chain F 2–149（148 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5	Resolution 2.50 Å R-free 0.279

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARGR_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–71； UniProt 79–149 Author chain B； PDBConstruct 1–71； UniProt 79–149 Author chain C； PDBConstruct 1–71； UniProt 79–149

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b4b
Deposition date deposition_date	1998-12-18
Structure title title	STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS
Keywords keywords	REPRESSOR, ARGININE, CORE, OLIGOMERIZATION DOMAIN, HELIX TURN HELIX; REPRESSOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.31 Å
Radius of gyration Rg (electron density) rg_electron	16.37 Å
Forward intensity I(0) i0	9562250.00
Molecular weight molecular_weight	23419.0 kDa
Excluded volume excluded_volume	29663 Å³
Envelope volume envelope_volume	32643 Å³
Hydration-shell volume shell_volume	16576 Å³
Envelope diameter envelope_diameter	51.4 Å
Shell Rg shell_rg	22.60 Å
Envelope Rg envelope_rg	16.58 Å
Shape Rg shape_rg	16.38 Å
Total Rg total_rg	17.38 Å
Total atoms total_atoms	1635
Residues n_residues	213
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	55.8 Å
Rg (real space) rg_real	17.19 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	9.5620e+06
I(0) uncertainty (real space) i0_real_error	1.1560e+05
Rg (reciprocal space) rg_reciprocal	17.21 Å
I(0) (reciprocal space) i0_reciprocal	9562000.0000
Solution quality estimate total_estimate	0.8033
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.121
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1736000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1b4ba_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
Family Family family	d.74.2.1 — C-terminal domain of arginine repressor

Domain ID domain_id	d1b4bb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
Family Family family	d.74.2.1 — C-terminal domain of arginine repressor

Domain ID domain_id	d1b4bc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.2 — C-terminal domain of arginine repressor
Family Family family	d.74.2.1 — C-terminal domain of arginine repressor

CATH v4.4 (3 domains)

Domain ID domain_id	1b4bA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1b4bB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1b4bC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

▶

8. Citations (2)

▶

Unit-cell length a length_a	82.000 Å
Unit-cell length b length_b	82.000 Å
Unit-cell length c length_c	67.200 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2660

Description description	ARGININE REPRESSOR
Molecular weight formula_weight	7640.9 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1835

STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS

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

ARGININE REPRESSOR

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	3

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	200

fit	/app/data/saxs_computation/b4/1b4b/1b4b.fit
pddf	/app/data/pr_computation/b4/1b4b/1b4b.pr.out
profile	/app/data/saxs_computation/b4/1b4b/1b4b.dat