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Yorodumi- PDB-3bjb: Crystal structure of a TetR transcriptional regulator from Rhodoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bjb | ||||||
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Title | Crystal structure of a TetR transcriptional regulator from Rhodococcus sp. RHA1 | ||||||
Components | Probable transcriptional regulator, TetR family protein | ||||||
Keywords | TRANSCRIPTION REGULATOR / APC7331 / TetR / Rhodococcus sp. RHA1 / 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 | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Tan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of a TetR transcriptional regulator from Rhodococcus sp. RHA1. Authors: Tan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bjb.cif.gz | 211.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bjb.ent.gz | 181.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bjb_validation.pdf.gz | 500.7 KB | Display | wwPDB validaton report |
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Full document | 3bjb_full_validation.pdf.gz | 544.3 KB | Display | |
Data in XML | 3bjb_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 3bjb_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjb ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjb | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23017.479 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: RHA1_ro05814 / Plasmid: p15Tv Lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q0S4E5 #2: Chemical | ChemComp-SO4 / #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: 2.51 Å3/Da / Density % sol: 50.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.5M Ammonnium sulfate, 0.1M Bis-Tris pH 6.5, 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: 0.97899, 0.97918 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007 / Details: Mirrors | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→32.46 Å / Num. all: 48913 / Num. obs: 48913 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 27.8 | |||||||||
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.8 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→32.46 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 25.035 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.487 / ESU R Free: 0.304 / 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: 66.869 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→32.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.57 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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