SAXSdb — 3qq6

▼

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

HTH-type transcriptional regulator sinR

Bacillus subtilis

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–69 Chain B； UniProt 1–69	Fragment：N-terminal domain of SinR residues 1-69	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M TRIS pH 8.5, 27% PEG3350, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.256
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–69	Fragment：N-terminal domain of SinR residues 1-69	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M TRIS pH 8.5, 27% PEG3350, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.256
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–69	Fragment：N-terminal domain of SinR residues 1-69	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1M TRIS pH 8.5, 27% PEG3350, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.256

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 3QQ6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B0N SINR PROTEIN/SINI PROTEIN COMPLEX Deposited 1998-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–111（111 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 1.90 Å R-free 0.245
1B0N SINR PROTEIN/SINI PROTEIN COMPLEX Deposited 1998-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–111（111 aa）	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 1.90 Å R-free 0.245
1B0N SINR PROTEIN/SINI PROTEIN COMPLEX Deposited 1998-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–111（111 aa）	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 1.90 Å R-free 0.245
1B0N SINR PROTEIN/SINI PROTEIN COMPLEX Deposited 1998-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–111（111 aa）	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 1.90 Å R-free 0.245
1B0N SINR PROTEIN/SINI PROTEIN COMPLEX Deposited 1998-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–111（111 aa）	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 1.90 Å R-free 0.245
1B0N SINR PROTEIN/SINI PROTEIN COMPLEX Deposited 1998-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–111（111 aa）	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 1.90 Å R-free 0.245
2YAL SinR, Master Regulator of biofilm formation in Bacillus subtilis Deposited 2011-02-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 75–111（37 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 75-111 Chain B 75–111（37 aa） Fragment：OLIGOMERISATION DOMAIN, RESIDUES 75-111	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；18% PEG MME2000, 0.16 M TRIS PH 8.5,0.01 M NI(II) CHLORIDE, 0.1 M MGCL2.	Resolution 2.27 Å R-free 0.435
3ZKC Crystal structure of the master regulator for biofilm formation SinR in complex with DNA. Deposited 2013-01-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–111（111 aa） Chain B 1–111（111 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；0.01M ZNCL2, 0.1M SODIUM ACTEATE, PH 5.0, 20% (W/V) PEG 6000	Resolution 3.00 Å R-free 0.264
5TN0 Solution Structure of the N-terminal DNA-binding domain of the master biofilm-regulator SinR from Bacillus subtilis Deposited 2016-10-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–69（69 aa） Fragment：residues 1-69	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 200；Pressure 1 NMR sample composition 1 mM [U-15N] SinrN, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] SinrN, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] SinRN, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided
5TN2 Solution Structure of the C-terminal multimerization domain of the master biofilm-regulator SinR from Bacillus subtilis Deposited 2016-10-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 69–111（43 aa） Fragment：residues 69-111 Chain B 69–111（43 aa） Fragment：residues 69-111 Chain C 69–111（43 aa） Fragment：residues 69-111 Chain D 69–111（43 aa） Fragment：residues 69-111	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 200；Pressure 1 NMR sample composition 1 mM [U-15N] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] SinRC, 20 mM MES, 200 mM sodium chloride, 0.02 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SINR_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–78； UniProt 1–69 Author chain B； PDBConstruct 10–78； UniProt 1–69

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	3qq6
Deposition date deposition_date	2011-02-15
Structure title title	The N-terminal DNA binding domain of SinR from Bacillus subtilis
Keywords keywords	Helix-Turn-Helix motif, biofilm, repressor, transcriptional regulator, SinI, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.79 Å
Radius of gyration Rg (electron density) rg_electron	15.82 Å
Forward intensity I(0) i0	4719880.00
Molecular weight molecular_weight	15608.0 kDa
Excluded volume excluded_volume	19568 Å³
Envelope volume envelope_volume	21968 Å³
Hydration-shell volume shell_volume	12356 Å³
Envelope diameter envelope_diameter	53.3 Å
Shell Rg shell_rg	20.68 Å
Envelope Rg envelope_rg	15.95 Å
Shape Rg shape_rg	15.78 Å
Total Rg total_rg	16.82 Å
Total atoms total_atoms	1100
Residues n_residues	136
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	54.4 Å
Rg (real space) rg_real	16.79 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	4.7200e+06
I(0) uncertainty (real space) i0_real_error	5.2130e+04
Rg (reciprocal space) rg_reciprocal	16.79 Å
I(0) (reciprocal space) i0_reciprocal	4720000.0000
Solution quality estimate total_estimate	0.8864
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.351
Kurtosis Kurtosis kurtosis	-0.319
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1065000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.992

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3qq6A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3qq6B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

▶

8. Citations (1)

▶

Unit-cell length a length_a	34.970 Å
Unit-cell length b length_b	45.329 Å
Unit-cell length c length_c	85.244 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	42.620 Å
R factor r_factor	0.2063
R_work r_work	0.2036
R_free r_free	0.2556

Description description	HTH-type transcriptional regulator sinR
Molecular weight formula_weight	8908.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1180

The N-terminal DNA binding domain of SinR from Bacillus subtilis

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

HTH-type transcriptional regulator sinR

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) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

fit	/app/data/saxs_computation/qq/3qq6/3qq6.fit
pddf	/app/data/pr_computation/qq/3qq6/3qq6.pr.out
profile	/app/data/saxs_computation/qq/3qq6/3qq6.dat