+Open data
-Basic information
Entry | Database: PDB / ID: 2yal | ||||||
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Title | SinR, Master Regulator of biofilm formation in Bacillus subtilis | ||||||
Components | HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATOR / ANTAGONIST / SPORULATION | ||||||
Function / homology | Function and homology information sporulation resulting in formation of a cellular spore / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Colledge, V.L. / Fogg, M.J. / Levdikov, V.M. / Leech, A. / Dodson, E.J. / Wilkinson, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structure and Organisation of Sinr, the Master Regulator of Biofilm Formation in Bacillus Subtilis. Authors: Colledge, V.L. / Fogg, M.J. / Levdikov, V.M. / Leech, A. / Dodson, E.J. / Wilkinson, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yal.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yal.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/2yal ftp://data.pdbj.org/pub/pdb/validation_reports/ya/2yal | HTTPS FTP |
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-Related structure data
Related structure data | 3qq6C 1bonS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.77051, 0.3865, 0.50689), Vector: |
-Components
#1: Protein/peptide | Mass: 4941.554 Da / Num. of mol.: 2 / Fragment: OLIGOMERISATION DOMAIN, RESIDUES 75-111 Source method: isolated from a genetically manipulated source Details: GPA TAG AT N-TERMINUS, NI BOUND BETWEEN N-TERMINI OF A CHAIN AND SYMMETRY EQUIVALENT OF THE B CHAIN Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06533 #2: Chemical | ChemComp-NI / | Nonpolymer details | NICKEL (NI): THERE IS AN ANOMALOUS SCATTERER ASSIGNED AS NI BRIDGING THE N-TERMINI OF THE A AND B CHAINS. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 18% PEG MME2000, 0.16 M TRIS PH 8.5,0.01 M NI(II) CHLORIDE, 0.1 M MGCL2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9789 |
Detector | Date: Oct 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 4405 / % possible obs: 85.7 % / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 59.6 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / % possible all: 42.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BON (A 74-110, B) Resolution: 2.27→41.72 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.836 / SU B: 34.725 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. THE GEOMETRY NEAR THE NI ATOM I ILL-DEFINED. HOWEVER THE PRESENCE OF NI IS CONFIRMED BY ANOMALOUS DIFFERENCE ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. THE GEOMETRY NEAR THE NI ATOM I ILL-DEFINED. HOWEVER THE PRESENCE OF NI IS CONFIRMED BY ANOMALOUS DIFFERENCE PATTERSONS. THE EXPERIMENTAL DATA IS NOT GOOD, AND THE R FACTOR HIGH. HOWEVER THE STRUCTURE REVEALS INTERESTING BIOCHEMICAL INSIGHTS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.717 Å2
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Refinement step | Cycle: LAST / Resolution: 2.27→41.72 Å
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Refine LS restraints |
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