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Yorodumi- PDB-3b6b: Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b6b | ||||||
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Title | Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with dGDP | ||||||
Components | Nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / NDK / PHOSPHOTRANSFERASE / NUCLEOTIDE BINDING PROTEIN / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Phosphorylation | ||||||
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: 2 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 | 3b6b.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b6b.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b6b_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 3b6b_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 3b6b_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3b6b_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/3b6b ftp://data.pdbj.org/pub/pdb/validation_reports/b6/3b6b | HTTPS FTP |
-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 (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Acanthamoeba polyphaga mimivirus / Gene: NDK / Plasmid: pDIGS02 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta pLysS / References: UniProt: Q5UQL3, nucleoside-diphosphate kinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-DGI / #4: Water | ChemComp-HOH / | |
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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: 2.57 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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98025 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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