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Yorodumi- PDB-3evm: Crystal structure of the Mimivirus NDK +Kpn-N62L-R107G triple mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3evm | ||||||
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Title | Crystal structure of the Mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with dCDP | ||||||
Components | Nucleoside diphosphate kinaseNucleoside-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 / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Acanthamoeba polyphaga mimivirus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 3evm.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3evm.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 3evm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/3evm ftp://data.pdbj.org/pub/pdb/validation_reports/ev/3evm | HTTPS FTP |
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-Related structure data
Related structure data | 2b8pC 2b8qC 3b6bC 3ddiC 3dkdC 3ee3C 3eicC 3ejmC 3elhC 3em1C 3emtC 3enaC 3etmC 3evoC 3evwC 3fbbC 3fbcC 3fbeC 3fbfC 3fc9C 3fcvC 3fcwC 3g2xC 3gp9C 3gpaC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16527.703 Da / Num. of mol.: 2 / Mutation: +Kpn, N62L, 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: 45.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.8 to 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: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å |
Detector | Type: KODAK / Detector: CCD / Date: Sep 24, 2007 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 24190 / % possible obs: 89.4 % / Redundancy: 7 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 564 / Rsym value: 0.305 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.228 Å / Occupancy max: 1 / Occupancy min: 0.86 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.61 / 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: 41.832 Å2 / ksol: 0.394 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.18 Å2 / Biso mean: 14.349 Å2 / Biso min: 0.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.228 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: 9
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