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Yorodumi- PDB-2b8q: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b8q | ||||||
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Title | X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with TDP | ||||||
Components | Probable nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / NDK / TDP / phosphotranferase | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mimivirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Jeudy, S. / Claverie, J.M. / Abergel, C. | ||||||
Citation | Journal: J.Virol. / Year: 2009 Title: Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase. Authors: Jeudy, S. / Lartigue, A. / Claverie, J.M. / Abergel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b8q.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b8q.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 2b8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/2b8q ftp://data.pdbj.org/pub/pdb/validation_reports/b8/2b8q | HTTPS FTP |
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-Related structure data
Related structure data | 2b8pSC 3b6bC 3ddiC 3dkdC 3ee3C 3eicC 3ejmC 3elhC 3em1C 3emtC 3enaC 3etmC 3evmC 3evoC 3evwC 3fbbC 3fbcC 3fbeC 3fbfC 3fc9C 3fcvC 3fcwC 3g2xC 3gp9C 3gpaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 16301.495 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mimivirus / Genus: Mimivirus / Gene: NDK / Plasmid: pDIGS02 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q5UQL3, nucleoside-diphosphate kinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TYD / #4: Chemical | ChemComp-PO4 / | #5: 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: 3.14 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 44% MPD, 0.1M hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 6, 2005 / Details: mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97565 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→66.5 Å / Num. obs: 39727 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2 / Rsym value: 0.355 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B8P Resolution: 2.5→29.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2483223.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REFMAC was also used for the refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.6874 Å2 / ksol: 0.324969 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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