[English] 日本語
![](img/lk-miru.gif)
- PDB-3g2x: Structure of mimivirus NDK +Kpn - N62L double mutant complexed wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3g2x | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of mimivirus NDK +Kpn - N62L double mutant complexed with dTDP | ||||||
![]() | Nucleoside diphosphate kinase | ||||||
![]() | TRANSFERASE / nucleoside diphosphate kinase 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 171.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 136.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 42.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b8pC ![]() 2b8qSC ![]() 3b6bC ![]() 3ddiC ![]() 3dkdC ![]() 3ee3C ![]() 3eicC ![]() 3ejmC ![]() 3elhC ![]() 3em1C ![]() 3emtC ![]() 3enaC ![]() 3etmC ![]() 3evmC ![]() 3evoC ![]() 3evwC ![]() 3fbbC ![]() 3fbcC ![]() 3fbeC ![]() 3fbfC ![]() 3fc9C ![]() 3fcvC ![]() 3fcwC ![]() 3gp9C ![]() 3gpaC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16627.846 Da / Num. of mol.: 6 / Mutation: +Kpn, N62L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TYD / #4: Water | ChemComp-HOH / | Sequence details | RESIDUES 92-94 ILT WERE REPLACED BY RESIDUES 92-98 TNPLASA. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.73 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD 40 to 45%, Hepes 0.1M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 14, 2007 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator Si (111), Si(311) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9205 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 31841 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 68.385 Å2 / Rsym value: 0.076 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4544 / Rsym value: 0.412 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2B8Q Resolution: 2.7→24.57 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.85 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.518 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107 Å2 / Biso mean: 51.712 Å2 / Biso min: 30.5 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→24.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
|