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Yorodumi- PDB-3evo: Crystal structure of the Mimivirus NDK +Kpn mutant complexed with dTDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3evo | ||||||
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Title | Crystal structure of the Mimivirus NDK +Kpn mutant complexed with dTDP | ||||||
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: 1.5 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 | 3evo.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3evo.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3evo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3evo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3evo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3evo_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 3evo_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/3evo ftp://data.pdbj.org/pub/pdb/validation_reports/ev/3evo | HTTPS FTP |
-Related structure data
Related structure data | 2b8pSC 2b8qC 3b6bC 3ddiC 3dkdC 3ee3C 3eicC 3ejmC 3elhC 3em1C 3emtC 3enaC 3etmC 3evmC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16628.791 Da / Num. of mol.: 2 / Mutation: +Kpn 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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 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: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2007 / Details: mirrors |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→35 Å / Num. obs: 43329 / % possible obs: 95.2 % / Redundancy: 6 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.036 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 3652 / Rsym value: 0.254 / % possible all: 74.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2b8p Resolution: 1.5→29.907 Å / Occupancy max: 1 / Occupancy min: 0.7 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.86 / 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: 48.399 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.36 Å2 / Biso mean: 18.421 Å2 / Biso min: 6.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.907 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: 16
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