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Yorodumi- PDB-3emt: Crystal structure of the mimivirus NDK +Kpn-R107G double mutant c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3emt | ||||||
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Title | Crystal structure of the mimivirus NDK +Kpn-R107G double mutant complexed with dGDP | ||||||
Components | Nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / phosphotransferase / nucleotide binding / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Phosphoprotein | ||||||
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 Similarity search - Function | ||||||
Biological species | Acanthamoeba polyphaga mimivirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jeudy, S. / Lartigue, A. / 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 | 3emt.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3emt.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 3emt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3emt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3emt_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3emt_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3emt_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3emt ftp://data.pdbj.org/pub/pdb/validation_reports/em/3emt | HTTPS FTP |
-Related structure data
Related structure data | 2b8pSC 2b8qC 3b6bC 3ddiC 3dkdC 3ee3C 3eicC 3ejmC 3elhC 3em1C 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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Unit cell |
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-Components
#1: Protein | Mass: 16528.648 Da / Num. of mol.: 2 / Mutation: +Kpn, R107G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R418, NDK / Plasmid: pDIGS02 / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta(DE3)pLysS / References: UniProt: Q5UQL3, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RESIDUES 92-94 ILT WERE REPLACED BY RESIDUES 92-98 TNPLASA. | |
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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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.8 to 1.1M Sodium Citrate, 0.1M Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2007 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→60.8 Å / Num. obs: 38246 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.685 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5578 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B8P Resolution: 1.6→60.806 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.86 / Phase error: 17.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.187 Å2 / ksol: 0.405 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.16 Å2 / Biso mean: 16.905 Å2 / Biso min: 6.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→60.806 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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