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Yorodumi- PDB-2guh: Crystal Structure of the Putative TetR-family Transcriptional Reg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2guh | ||||||
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Title | Crystal Structure of the Putative TetR-family Transcriptional Regulator from Rhodococcus sp. RHA1 | ||||||
Components | Putative TetR-family transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / helix-turn-helix / tetR fold / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å | ||||||
Authors | Kim, Y. / Joachimiak, A. / Skarina, T. / Zheng, H. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putative TetR-family Transcriptional Regulator from Rhodococcus sp. RHA1 Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Zheng, H. / Edwards, A. / Savchenko, A. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the protein has not been deposited into any sequence database at the time ...SEQUENCE The sequence of the protein has not been deposited into any sequence database at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2guh.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2guh.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 2guh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2guh_validation.pdf.gz | 454.8 KB | Display | wwPDB validaton report |
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Full document | 2guh_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 2guh_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 2guh_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/2guh ftp://data.pdbj.org/pub/pdb/validation_reports/gu/2guh | 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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Unit cell |
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-Components
#1: Protein | Mass: 24005.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: rha6424 / Plasmid: modified pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q0S8Y3 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: 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: 2.12 Å3/Da / Density % sol: 42.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25 % PEG3350, 0.2M MgCl2, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97872 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Apr 20, 2006 / Details: mirror |
Radiation | Monochromator: double crystal monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→23.37 Å / Num. all: 64582 / Num. obs: 63688 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3100 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.52→23.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.175 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.302 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→23.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.519→1.559 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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