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Yorodumi- PDB-1wwm: Crystal Structure of Conserved Hypothetical Protein TT2028 from a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wwm | ||||||
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Title | Crystal Structure of Conserved Hypothetical Protein TT2028 from an Extremely Thermophilic Bacterium Thermus thermophilus HB8 | ||||||
Components | hypothetical protein TT2028Hypothesis | ||||||
Keywords | TRANSCRIPTION / TenA/Thi-4 family / putative transctiption activator / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å | ||||||
Authors | Mizohata, E. / Ushikoshi-Nakayama, R. / Terada, T. / Murayama, K. / Sakai, H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of TT2028 from an Extremely Thermophilic Bacterium Thermus thermophilus HB8 Authors: Mizohata, E. / Ushikoshi-Nakayama, R. / Terada, T. / Murayama, K. / Sakai, H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wwm.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wwm.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/1wwm ftp://data.pdbj.org/pub/pdb/validation_reports/ww/1wwm | HTTPS FTP |
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-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: 22268.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SLX4 #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: 2.43 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: MES, PEG8000, magnesium acetate, pH 6.9, 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: 0.96200, 0.97904, 0.97932 | ||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 20, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→50 Å / Num. obs: 24268 / Biso Wilson estimate: 13.5 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.61→30.65 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 180963.2 / 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: 40.8882 Å2 / ksol: 0.360115 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.61→30.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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