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Yorodumi- PDB-1wkj: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wkj | ||||||
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Title | Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 | ||||||
Components | nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / nucleoside diphosphate kinase / Thermus thermophilus HB8 / kinase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Takeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 Authors: Takeishi, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wkj.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wkj.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wkj ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wkj | HTTPS FTP |
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-Related structure data
Related structure data | 1wkkC 1wklC 1hhqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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 hexamer generated from the dimer in the asymmetric unit by the operations: -y+1, x-y+1, z and -x+y, -x+1, z. |
-Components
#1: Protein | Mass: 15366.903 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ndk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLV5, nucleoside-diphosphate kinase #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: 3.8 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 10% PEG4000, 0.09M Ammonium Acetate, 15% Glycerol, 0.1M Sodium Citrate, pH 5.2, 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: BL45XU / Wavelength: 0.98 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 387285 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 39 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 12.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHQ Resolution: 2→50 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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