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Yorodumi- PDB-3em1: Crystal structure of the mimivirus NDK +Kpn-N62L double mutant co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3em1 | ||||||
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Title | Crystal structure of the mimivirus NDK +Kpn-N62L double mutant complexed with dTDP | ||||||
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 / 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 | 3em1.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3em1.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 3em1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3em1 ftp://data.pdbj.org/pub/pdb/validation_reports/em/3em1 | HTTPS FTP |
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-Related structure data
Related structure data | 2b8pSC 2b8qC 3b6bC 3ddiC 3dkdC 3ee3C 3eicC 3ejmC 3elhC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16627.846 Da / Num. of mol.: 2 / Mutation: +Kpn, N62L 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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 1M sodium citrate, 0.1M Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9205 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 11, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9205 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→60.971 Å / Num. obs: 46603 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 17.904 Å2 / Rsym value: 0.06 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 6771 / Rsym value: 0.297 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B8P Resolution: 1.5→29.235 Å / Occupancy max: 1 / Occupancy min: 0.61 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 18.5 / 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: 44.735 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.93 Å2 / Biso mean: 18.7 Å2 / Biso min: 7.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.235 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: 17
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