[English] 日本語
![](img/lk-miru.gif)
- PDB-1nb2: Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1nb2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans | ||||||
![]() | Nucleoside Diphosphate Kinase | ||||||
![]() | TRANSFERASE / Nucleoside Diphosphate Kinase / Bacillus Halodenitrifians | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, C.-J. / Liu, M.-Y. / Chang, W.-C. / Chang, T. / Wang, B.-C. / Le Gall, J. | ||||||
![]() | ![]() Title: Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase. Authors: Chen, C.-J. / Liu, M.-Y. / Chang, T. / Chang, W.-C. / Wang, B.-C. / Le Gall, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 37.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 368.5 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 6||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the crystallographic operations. |
-
Components
#1: Protein | Mass: 14883.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q7SIA9, nucleoside-diphosphate kinase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.39 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Sodium Formate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2001 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 24296 / Num. obs: 21145 / % possible obs: 87.03 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rsym value: 0.056 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 813 / Rsym value: 0.26 / % possible all: 64 |
Reflection | *PLUS % possible obs: 95.6 % / Redundancy: 7.03 % / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 64 % / Mean I/σ(I) obs: 3.8 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.211 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |