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Yorodumi- PDB-2nx4: The Crystal Structure of athe Putative TetR-family transcriptiona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nx4 | ||||||
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Title | The Crystal Structure of athe Putative TetR-family transcriptional regulator Rha06780 from Rhodococcus sp. Rha1. | ||||||
Components | Transcriptional regulator, TetR family protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / tetR / HTH DNA binding motif / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Rhodococcus sp. RHA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Zhang, R. / Evdokimova, E. / Kudritskam, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published / Year: 2006 Title: The Crystal Structure of a TetR-family transcriptional regulator from Rhodococcus sp. Authors: Zhang, R. / Evdokimova, E. / Kudritskam, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nx4.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nx4.ent.gz | 133.8 KB | Display | PDB format |
PDBx/mmJSON format | 2nx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nx4_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 2nx4_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 2nx4_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 2nx4_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nx4 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nx4 | HTTPS FTP |
-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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2 |
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Unit cell |
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Details | This protein exist as dimer. There are two dimers (A/B, C/D) in the asymmetric unit. |
-Components
#1: Protein | Mass: 21762.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. RHA1 (bacteria) / Strain: Rha1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0SCU8 #2: 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: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.2M Ammonium Formate, 26% PEG3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→69.01 Å / Num. all: 88630 / Num. obs: 85617 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.46 |
Reflection shell | Resolution: 1.7→1.742 Å / Redundancy: 2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.2 / Num. unique all: 6412 / % possible all: 79.15 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.241 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.108 / ESU R Free: 0.106 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 18.284 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 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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