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- PDB-3eic: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eic | ||||||
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Title | X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with UDP | ||||||
![]() | Nucleoside diphosphate kinase | ||||||
![]() | TRANSFERASE / NDK 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 | ![]() | 173.9 KB | Display | ![]() |
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PDB format | ![]() | 139 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b8pC ![]() 2b8qSC ![]() 3b6bC ![]() 3ddiC ![]() 3dkdC ![]() 3ee3C ![]() 3ejmC ![]() 3elhC ![]() 3em1C ![]() 3emtC ![]() 3enaC ![]() 3etmC ![]() 3evmC ![]() 3evoC ![]() 3evwC ![]() 3fbbC ![]() 3fbcC ![]() 3fbeC ![]() 3fbfC ![]() 3fc9C ![]() 3fcvC ![]() 3fcwC ![]() 3g2xC ![]() 3gp9C ![]() 3gpaC C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Details | hexamer |
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Components
#1: Protein | Mass: 16301.495 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-UDP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.66 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: MPD 40 to 44%, MOPS 0.1M, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2007 / Details: mirrors |
Radiation | Monochromator: Si 311 and Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.064 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→92.4 Å / Num. obs: 49557 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 47.885 Å2 / Rsym value: 0.071 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7285 / Rsym value: 0.331 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2b8q Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.06 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.298 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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