[English] 日本語
Yorodumi- PDB-2b8p: Crystal structure of Acanthamoeba polyphaga mimivirus NDK, the fi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b8p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Acanthamoeba polyphaga mimivirus NDK, the first viral nucleoside diphosphate kinase | ||||||
Components | Probable nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / NDK / phosphotransferase / nucleotide binding | ||||||
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 | Mimivirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Jeudy, S. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2b8p.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2b8p.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 2b8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/2b8p ftp://data.pdbj.org/pub/pdb/validation_reports/b8/2b8p | HTTPS FTP |
---|
-Related structure data
Related structure data | 2b8qC 3b6bC 3ddiC 3dkdC 3ee3C 3eicC 3ejmC 3elhC 3em1C 3emtC 3enaC 3etmC 3evmC 3evoC 3evwC 3fbbC 3fbcC 3fbeC 3fbfC 3fc9C 3fcvC 3fcwC 3g2xC 3gp9C 3gpaC 1k44S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 18174.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mimivirus / Genus: Mimivirus / Gene: NDK / Plasmid: pDIGS02 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q5UQL3, nucleoside-diphosphate kinase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ammonium sulfate 1.6M, MES 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97563 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 3, 2004 / Details: mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97563 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→70.36 Å / Num. obs: 8922 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.256 / % possible all: 94.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K44 Resolution: 2.55→24.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1541510.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1508 Å2 / ksol: 0.376597 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→24.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|