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Yorodumi- PDB-2d6y: Crystal Structure of transcriptional factor SCO4008 from Streptom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d6y | ||||||
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Title | Crystal Structure of transcriptional factor SCO4008 from Streptomyces coelicolor A3(2) | ||||||
Components | putative tetR family regulatory protein | ||||||
Keywords | GENE REGULATION / Helix-turn-Helix | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Hayashi, T. / Tanaka, Y. / Sakai, N. / Yao, M. / Tamura, T. / Tanaka, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: SCO4008, a Putative TetR Transcriptional Repressor from Streptomyces coelicolor A3(2), Regulates Transcription of sco4007 by Multidrug Recognition. Authors: Hayashi, T. / Tanaka, Y. / Sakai, N. / Okada, U. / Yao, M. / Watanabe, N. / Tamura, T. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d6y.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d6y.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 2d6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/2d6y ftp://data.pdbj.org/pub/pdb/validation_reports/d6/2d6y | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22853.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO4008 / Plasmid: pTip-QC1 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L-88 / References: UniProt: Q9ADP7 #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: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20mM Tris-HCl, 16% PEG350, 420mM di-ammonium tertrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 18542 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.06 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.5 % / Num. unique all: 1742 / Rsym value: 0.247 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→19.86 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1549453.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.4191 Å2 / ksol: 0.350651 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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