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Yorodumi- PDB-2dg6: Crystal structure of the putative transcriptional regulator SCO55... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dg6 | ||||||
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Title | Crystal structure of the putative transcriptional regulator SCO5550 from Streptomyces coelicolor A3(2) | ||||||
Components | putative transcriptional regulator | ||||||
Keywords | GENE REGULATION / Winged-helix motif / MerR family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Hayashi, T. / Tanaka, Y. / Sakai, N. / Yao, M. / Tamura, T. / Tanaka, I. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2013 Title: Structural and genomic DNA analysis of a putative transcription factor SCO5550 from Streptomyces coelicolor A3(2): regulating the expression of gene sco5551 as a transcriptional activator with a novel dimer shape Authors: Hayashi, T. / Tanaka, Y. / Sakai, N. / Watanabe, N. / Tamura, T. / Tanaka, I. / Yao, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dg6.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dg6.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dg6_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 2dg6_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 2dg6_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 2dg6_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/2dg6 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/2dg6 | HTTPS FTP |
-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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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, -y+1, z. |
-Components
#1: Protein | Mass: 25211.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L-88 / References: GenBank: 3355698, UniProt: O86531*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM Bis-Tris pH6.5, 1250mM Ammonium sulfate, 150mM NaCl, 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: 0.9788, 0.9795, 0.900 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2005 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 11793 / % possible obs: 98.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.072 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.3 % / Num. unique all: 1041 / Rsym value: 0.224 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→19.95 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1510278.22 / 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: 55.6542 Å2 / ksol: 0.389945 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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