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5tmx

Solution Structure of SinI, antagonist to the master biofilm-regulator SinR in Bacillus subtilis

Method: SOLUTION NMR Dmax: 66.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein SinI

Bacillus subtilis (strain 168)

UniProt P23308

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 1–57 Chain B； UniProt 1–57 Fragment：residues 1-57 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] SinI, 20 mM MES, 200 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-13C; U-15N] SinI, 20 mM MES, 200 mM NaCl, 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 5TMX 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 B 1–57（57 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 B 1–57（57 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 B 1–57（57 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 B 1–57（57 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 B 1–57（57 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 B 1–57（57 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

1 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SINI_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–63； UniProt 1–57 Author chain B； PDBConstruct 7–63； UniProt 1–57

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 5tmx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5tmx
Deposition date deposition_date2016-10-13
Structure title titleSolution Structure of SinI, antagonist to the master biofilm-regulator SinR in Bacillus subtilis
Keywords keywordssporulation, repressor, biofilm, TRANSCRIPTION REGULATOR; TRANSCRIPTION REGULATOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.51 Å
Radius of gyration Rg (electron density) rg_electron24.75 Å
Forward intensity I(0) i0316725000.00
Molecular weight molecular_weight143420.0 kDa
Excluded volume excluded_volume177960 ų
Envelope volume envelope_volume116950 ų
Hydration-shell volume shell_volume30652 ų
Envelope diameter envelope_diameter118.2 Å
Shell Rg shell_rg38.10 Å
Envelope Rg envelope_rg34.26 Å
Shape Rg shape_rg24.72 Å
Total Rg total_rg25.49 Å
Total atoms total_atoms19980
Residues n_residues1260
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 dmax66.9 Å
Rg (real space) rg_real23.33 Å
Rg uncertainty (real space) rg_real_error0.14 Å
I(0) (real space) i0_real3.0010e+08
I(0) uncertainty (real space) i0_real_error3.0340e+06
Rg (reciprocal space) rg_reciprocal25.86 Å
I(0) (reciprocal space) i0_reciprocal316700000.0000
Solution quality estimate total_estimate0.6675
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary18.3 Å
Skewness Skewness skewness0.327
Kurtosis Kurtosis kurtosis-0.731
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha2.4120
Highest regularization parameter α highest_alpha1056000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.005; Oscil: 0.976; Stabil: 0.986; Sysdev: 0.000; Positv: 1.000; Valcen: 0.802; 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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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5tmxa1
Class classa — All alpha proteins
Fold Fold folda.34 — Dimerisation interlock
Superfamily Superfamily superfamilya.34.1 — SinR repressor dimerisation domain-like
Family Family familya.34.1.1 — SinR repressor dimerisation domain-like
Domain ID domain_idd5tmxa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5tmxb1
Class classa — All alpha proteins
Fold Fold folda.34 — Dimerisation interlock
Superfamily Superfamily superfamilya.34.1 — SinR repressor dimerisation domain-like
Family Family familya.34.1.1 — SinR repressor dimerisation domain-like
Domain ID domain_idd5tmxb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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8. Citations (1)

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9. Files and Curves (10)