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Yorodumi- PDB-2h0a: Crystal structure of probable Transcription regulator from Thermu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h0a | ||||||
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Title | Crystal structure of probable Transcription regulator from Thermus thermophilus | ||||||
Components | Transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / regulator / repressor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Kumarevel, T.S. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8. Authors: Kumarevel, T.S. / Tanaka, T. / Shinkai, A. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h0a.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h0a.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 2h0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h0a_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 2h0a_full_validation.pdf.gz | 431.2 KB | Display | |
Data in XML | 2h0a_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2h0a_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/2h0a ftp://data.pdbj.org/pub/pdb/validation_reports/h0/2h0a | 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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-Components
#1: Protein | Mass: 30674.016 Da / Num. of mol.: 1 / Fragment: TT1016 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SK45 |
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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: 3.13 Å3/Da / Density % sol: 60.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ethanol, Tris, MgCl2, pH 8.5, 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: BL26B1 / Wavelength: 1.00, 0.9789, 0.9793, 0.9950 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2005 | |||||||||||||||
Radiation | Monochromator: Silicon II channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→50 Å / Num. all: 22920 / Num. obs: 22920 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.2 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.086 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.539 / Num. unique all: 2290 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→19.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 105263.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.6188 Å2 / ksol: 0.304208 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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