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Yorodumi- PDB-3d8u: The crystal structure of a PurR family transcriptional regulator ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d8u | ||||||
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Title | The crystal structure of a PurR family transcriptional regulator from Vibrio parahaemolyticus RIMD 2210633 | ||||||
Components | PurR transcriptional regulator | ||||||
Keywords | transcription regulator / APC91343.1 / PurR / transcriptional regulator / Vibrio parahaemolyticus RIMD 2210633 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / DNA-binding / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.88 Å | ||||||
Authors | Tan, K. / Hatzos, C. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a PurR family transcriptional regulator from Vibrio parahaemolyticus RIMD 2210633 Authors: Tan, K. / Hatzos, C. / Moy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d8u.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d8u.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 3d8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/3d8u ftp://data.pdbj.org/pub/pdb/validation_reports/d8/3d8u | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | authors state that the biological assembly is experimentally unknown. The chains A and B are predicted to form a dimer. |
-Components
#1: Protein | Mass: 30523.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA0232 / Plasmid: pMCSG8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q87JL7 |
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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: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.0M sodium citrate 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945, 0.97959 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2007 / Details: Mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.88→41.3 Å / Num. all: 17527 / Num. obs: 17527 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 30.2 | |||||||||
Reflection shell | Resolution: 2.88→2.95 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 1.8 / Num. unique all: 993 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.88→41.3 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 32.729 / SU ML: 0.29 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.345 / ESU R Free: 0.405 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.88→41.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.879→2.954 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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