SAXSdb — 2yal

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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 75–111 Chain B； UniProt 75–111	Fragment：OLIGOMERISATION DOMAIN, RESIDUES 75-111	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

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 2YAL	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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
3QQ6 The N-terminal DNA binding domain of SinR from Bacillus subtilis Deposited 2011-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–69（69 aa） Fragment：N-terminal domain of SinR residues 1-69 Chain B 1–69（69 aa） Fragment：N-terminal domain of SinR residues 1-69	Not recorded	No recorded non-water small molecule	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
3QQ6 The N-terminal DNA binding domain of SinR from Bacillus subtilis Deposited 2011-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–69（69 aa） Fragment：N-terminal domain of SinR residues 1-69	Not recorded	No recorded non-water small molecule	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
3QQ6 The N-terminal DNA binding domain of SinR from Bacillus subtilis Deposited 2011-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–69（69 aa） Fragment：N-terminal domain of SinR residues 1-69	Not recorded	No recorded non-water small molecule	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
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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 12 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 5–41； UniProt 75–111 Author chain B； PDBConstruct 5–41； UniProt 75–111

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	2yal
Deposition date deposition_date	2011-02-23
Structure title title	SinR, Master Regulator of biofilm formation in Bacillus subtilis
Keywords keywords	TRANSCRIPTION, TRANSCRIPTION REGULATOR, ANTAGONIST, SPORULATION; TRANSCRIPTION
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	13.93 Å
Radius of gyration Rg (electron density) rg_electron	12.49 Å
Forward intensity I(0) i0	1888870.00
Molecular weight molecular_weight	9250.0 kDa
Excluded volume excluded_volume	11542 Å³
Envelope volume envelope_volume	12958 Å³
Hydration-shell volume shell_volume	9250 Å³
Envelope diameter envelope_diameter	43.4 Å
Shell Rg shell_rg	17.64 Å
Envelope Rg envelope_rg	12.87 Å
Shape Rg shape_rg	12.43 Å
Total Rg total_rg	13.88 Å
Total atoms total_atoms	650
Residues n_residues	77
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	45.6 Å
Rg (real space) rg_real	13.86 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.8890e+06
I(0) uncertainty (real space) i0_real_error	2.3130e+04
Rg (reciprocal space) rg_reciprocal	13.87 Å
I(0) (reciprocal space) i0_reciprocal	1889000.0000
Solution quality estimate total_estimate	0.8802
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.194
Kurtosis Kurtosis kurtosis	-0.264
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	258300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.971

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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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8. Citations (1)

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Unit-cell length a length_a	36.117 Å
Unit-cell length b length_b	36.117 Å
Unit-cell length c length_c	250.342 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.270 Å
Low-resolution limit resolution_low	41.720 Å
R factor r_factor	0.2892
R_work r_work	0.2834
R_free r_free	0.4348

Description description	HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR
Molecular weight formula_weight	4941.6 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	650

SinR, Master Regulator of biofilm formation in 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 non-polymer

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	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/ya/2yal/2yal.fit
pddf	/app/data/pr_computation/ya/2yal/2yal.pr.out
profile	/app/data/saxs_computation/ya/2yal/2yal.dat