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Yorodumi- PDB-4q11: Crystal structure of Proteus mirabilis transcriptional regulator ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q11 | ||||||
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Title | Crystal structure of Proteus mirabilis transcriptional regulator protein Crl at 1.95A resolution | ||||||
Components | Sigma factor-binding protein Crl | ||||||
Keywords | Transcription regulator / sigma factor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Proteus mirabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Norel, F. / Mayer, C. / Saul, F.A. / Haouz, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Structural and functional features of Crl proteins and identification of conserved surface residues required for interaction with the RpoS/ sigma S subunit of RNA polymerase. Authors: Cavaliere, P. / Levi-Acobas, F. / Mayer, C. / Saul, F.A. / England, P. / Weber, P. / Raynal, B. / Monteil, V. / Bellalou, J. / Haouz, A. / Norel, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q11.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q11.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 4q11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/4q11 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/4q11 | HTTPS FTP |
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-Related structure data
Related structure data | 3rpjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15764.120 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: crl, PMI0368 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B4EUU9 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.82 Å3/Da / Density % sol: 32.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 100mM CHES-NaOH, PEG3000 30%(w/v), pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30.25 Å / Num. all: 16783 / Num. obs: 16783 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1185 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RPJ Resolution: 1.95→30.25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.329 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.639 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30.25 Å
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Refine LS restraints |
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