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- PDB-3ena: Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ena | ||||||
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Title | Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with dGDP | ||||||
![]() | Nucleoside diphosphate kinase | ||||||
![]() | TRANSFERASE / phosphotransferase nucleotide binding / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Phosphoprotein | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeudy, S. / Lartigue, A. / Claverie, J.M. / Abergel, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.1 KB | Display | ![]() |
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PDB format | ![]() | 53.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b8pSC ![]() 2b8qC ![]() 3b6bC ![]() 3ddiC ![]() 3dkdC ![]() 3ee3C ![]() 3eicC ![]() 3ejmC ![]() 3elhC ![]() 3em1C ![]() 3emtC ![]() 3etmC ![]() 3evmC ![]() 3evoC ![]() 3evwC ![]() 3fbbC ![]() 3fbcC ![]() 3fbeC ![]() 3fbfC ![]() 3fc9C ![]() 3fcvC ![]() 3fcwC ![]() 3g2xC ![]() 3gp9C ![]() 3gpaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.44 % |
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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: ![]() ![]() ![]() |
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→52.6 Å / Num. obs: 38444 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 16.26 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5608 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2B8P Resolution: 1.6→52.611 Å / Occupancy max: 1 / Occupancy min: 0.9 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.6 / Phase error: 18.2 / 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: 50.181 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.13 Å2 / Biso mean: 16.354 Å2 / Biso min: 6.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→52.611 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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