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5tn2

Solution Structure of the C-terminal multimerization domain of the master biofilm-regulator SinR from Bacillus subtilis

Method: SOLUTION NMR Dmax: 67.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HTH-type transcriptional regulator SinR

Bacillus subtilis (strain 168)

UniProt P06533

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 69–111 Chain B； UniProt 69–111 Chain C； UniProt 69–111 Chain D； UniProt 69–111 Fragment：residues 69-111 No other associated polymer 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

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 5TN2 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 method 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 method 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 method 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 method 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 method 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 method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
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 experimental method 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 experimental method 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 experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 experimental conditions 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

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 5–47； UniProt 69–111 Author chain B； PDBConstruct 5–47； UniProt 69–111 Author chain C； PDBConstruct 5–47； UniProt 69–111 Author chain D； PDBConstruct 5–47； UniProt 69–111

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5tn2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tn2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tn2
Deposition date deposition_date2016-10-13
Structure title titleSolution Structure of the C-terminal multimerization domain of the master biofilm-regulator SinR from Bacillus subtilis
Keywords keywordsbiofilm formation, multimerization domain, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.44 Å
Radius of gyration Rg (electron density) rg_electron18.46 Å
Forward intensity I(0) i0814822000.00
Molecular weight molecular_weight228450.0 kDa
Excluded volume excluded_volume280660 ų
Envelope volume envelope_volume61208 ų
Hydration-shell volume shell_volume23316 ų
Envelope diameter envelope_diameter78.5 Å
Shell Rg shell_rg29.04 Å
Envelope Rg envelope_rg22.66 Å
Shape Rg shape_rg18.41 Å
Total Rg total_rg18.90 Å
Total atoms total_atoms31320
Residues n_residues1880
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.6 Å
Rg (real space) rg_real19.45 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real8.1480e+08
I(0) uncertainty (real space) i0_real_error1.1280e+07
Rg (reciprocal space) rg_reciprocal19.44 Å
I(0) (reciprocal space) i0_reciprocal814800000.0000
Solution quality estimate total_estimate0.7837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary60.9 Å
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.237
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3173000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.762; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)