1b4a

STRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS

Method: X-RAY DIFFRACTION D_max: 93.6 Å Quality: GOOD

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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 2–149 Chain B； UniProt 2–149 Chain C； UniProt 2–149 Chain D； UniProt 2–149 Chain E； UniProt 2–149 Chain F； UniProt 2–149	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；pH 5	Resolution 2.50 Å R-free 0.279

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 1B4A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4B STRUCTURE OF THE OLIGOMERIZATION DOMAIN 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 79–149（71 aa） Fragment：OLIGOMERIZATION DOMAIN, L-ARGININE BINDING DOMAIN Chain B 79–149（71 aa） Fragment：OLIGOMERIZATION DOMAIN, L-ARGININE BINDING DOMAIN Chain C 79–149（71 aa） Fragment：OLIGOMERIZATION DOMAIN, L-ARGININE BINDING DOMAIN	Not recorded	ARG ARGININE × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.266

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 2–149； UniProt 2–149 Author chain B； PDBConstruct 2–149； UniProt 2–149 Author chain C； PDBConstruct 2–149； UniProt 2–149 Author chain D； PDBConstruct 2–149； UniProt 2–149 Author chain E； PDBConstruct 2–149； UniProt 2–149 Author chain F； PDBConstruct 2–149； UniProt 2–149

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b4a
Deposition date deposition_date	1998-12-18
Structure title title	STRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS
Keywords keywords	REPRESSOR, ARGININE, HELIX TURN HELIX; REPRESSOR
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	30.19 Å
Radius of gyration Rg (electron density) rg_electron	29.05 Å
Forward intensity I(0) i0	154604000.00
Molecular weight molecular_weight	98593.0 kDa
Excluded volume excluded_volume	123930 Å³
Envelope volume envelope_volume	159970 Å³
Hydration-shell volume shell_volume	44820 Å³
Envelope diameter envelope_diameter	99.5 Å
Shell Rg shell_rg	37.33 Å
Envelope Rg envelope_rg	28.68 Å
Shape Rg shape_rg	29.07 Å
Total Rg total_rg	29.76 Å
Total atoms total_atoms	6900
Residues n_residues	876
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	93.6 Å
Rg (real space) rg_real	30.00 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.5460e+08
I(0) uncertainty (real space) i0_real_error	2.0770e+06
Rg (reciprocal space) rg_reciprocal	30.09 Å
I(0) (reciprocal space) i0_reciprocal	154600000.0000
Solution quality estimate total_estimate	0.8963
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.8 Å
Skewness Skewness skewness	0.156
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27230000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.974

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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) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1b4aa1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

Domain ID domain_id	d1b4aa2
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	d1b4ab1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

Domain ID domain_id	d1b4ab2
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	d1b4ac1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

Domain ID domain_id	d1b4ac2
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	d1b4ad1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

Domain ID domain_id	d1b4ad2
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	d1b4ae1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

Domain ID domain_id	d1b4ae2
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	d1b4af1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.3 — Arginine repressor (ArgR), N-terminal DNA-binding domain

Domain ID domain_id	d1b4af2
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 (12 domains)

Domain ID domain_id	1b4aA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b4aA02
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	1b4aB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b4aB02
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	1b4aC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b4aC02
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	1b4aD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b4aD02
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	1b4aE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b4aE02
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	1b4aF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1b4aF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

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8. Citations (2)

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Unit-cell length a length_a	72.800 Å
Unit-cell length b length_b	121.900 Å
Unit-cell length c length_c	227.400 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2790

Description description	ARGININE REPRESSOR
Molecular weight formula_weight	16809.5 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7487

STRUCTURE 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	587

fit	/app/data/saxs_computation/b4/1b4a/1b4a.fit
pddf	/app/data/pr_computation/b4/1b4a/1b4a.pr.out
profile	/app/data/saxs_computation/b4/1b4a/1b4a.dat