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Yorodumi- PDB-1wjg: Crystal structure of a probable ATP binding protein from thermus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wjg | ||||||
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Title | Crystal structure of a probable ATP binding protein from thermus themophilus HB8 | ||||||
Components | probable ATP binding protein | ||||||
Keywords | PROTEIN BINDING / ATP BINDING PROTEIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Iino, H. / Yao, M. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a probable atp binding protein from thermus themophilus HB8 Authors: Iino, H. / Yao, M. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wjg.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wjg.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 1wjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/1wjg ftp://data.pdbj.org/pub/pdb/validation_reports/wj/1wjg | 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: 14775.985 Da / Num. of mol.: 1 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: Q5SJV7 |
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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: 2.4 Å3/Da / Density % sol: 48.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 20% PEG200, 0.1M MES, 0.04M Strontium chloride, pH 5.7, 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: BL26B2 / Wavelength: 0.97898, 0.97927, 0.98200 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 4, 2003 | ||||||||||||
Radiation | Monochromator: SILICON DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→43.4 Å / Num. obs: 11879 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 43.6 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 9.9 / Num. unique all: 11879 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1521079.64 / 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: 38.5986 Å2 / ksol: 0.358973 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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