[English] 日本語
![](img/lk-miru.gif)
- PDB-3etm: Crystal structure of the mimivirus NDK +KPN-N62L-R107G triple mut... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3etm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the mimivirus NDK +KPN-N62L-R107G triple mutant complexed with CDP | ||||||
![]() | Nucleoside diphosphate kinase | ||||||
![]() | TRANSFERASE / 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 | ![]() | 73.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b8pSC ![]() 2b8qC ![]() 3b6bC ![]() 3ddiC ![]() 3dkdC ![]() 3ee3C ![]() 3eicC ![]() 3ejmC ![]() 3elhC ![]() 3em1C ![]() 3emtC ![]() 3enaC ![]() 3evmC ![]() 3evoC ![]() 3evwC ![]() 3fbbC ![]() 3fbcC ![]() 3fbeC ![]() 3fbfC ![]() 3fc9C ![]() 3fcvC ![]() 3fcwC ![]() 3g2xC ![]() 3gp9C ![]() 3gpaC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 16527.703 Da / Num. of mol.: 2 / Mutation: +Kpn, N62L, R107G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #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: 2.25 Å3/Da / Density % sol: 45.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.8 to 1M sodium citrate, 0.1M Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Sep 27, 2007 |
Radiation | Monochromator: Cu radiation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.4 Å / Num. obs: 22776 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 12.663 Å2 / Rsym value: 0.094 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2150 / Rsym value: 0.332 / % possible all: 94.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2B8P Resolution: 1.9→29.231 Å / Occupancy max: 1 / Occupancy min: 0.95 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.5 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.479 Å2 / ksol: 0.367 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.2 Å2 / Biso mean: 15.22 Å2 / Biso min: 2.9 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.231 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
|