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- PDB-3b6b: Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b6b | ||||||
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Title | Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP | ||||||
![]() | Nucleoside diphosphate kinase | ||||||
![]() | TRANSFERASE / NDK / PHOSPHOTRANSFERASE / NUCLEOTIDE BINDING PROTEIN / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Phosphorylation | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
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 | ![]() | 177.8 KB | Display | ![]() |
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PDB format | ![]() | 141.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2b8pC ![]() 2b8qC ![]() 3ddiC ![]() 3dkdC ![]() 3ee3C ![]() 3eicC ![]() 3ejmC ![]() 3elhC ![]() 3em1C ![]() 3emtC ![]() 3enaC ![]() 3etmC ![]() 3evmC ![]() 3evoC ![]() 3evwC ![]() 3fbbC ![]() 3fbcC ![]() 3fbeC ![]() 3fbfC ![]() 3fc9C ![]() 3fcvC ![]() 3fcwC ![]() 3g2xC ![]() 3gp9C ![]() 3gpaC ![]() 1b8qS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18174.498 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-DGI / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 40-45% MPD, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98025 Å / Relative weight: 1 |
Reflection | Resolution: 2→76 Å / Num. obs: 72791 / % possible obs: 98.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.6 / Num. unique all: 10642 / Rsym value: 0.303 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B8Q Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.611 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.145 / 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: 33.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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