[English] 日本語
![](img/lk-miru.gif)
- PDB-3q86: Crystal structure of Staphylococcus aureus nucleoside diphosphate... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3q86 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with GTP | ||||||
![]() | Nucleoside diphosphate kinase | ||||||
![]() | TRANSFERASE / Ferridoxin fold / alpha-beta protein family / Nucleoside diphosphate kinases (NDKs) / transfer / a gamma phosphate / nucleoside triphosphates / nucleoside diphosphate / Nucleotide binding Magnesium / Metal binding / Phosphorylation | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Srivastava, S.K. / Rajasree, K. / Gopal, B. | ||||||
![]() | ![]() Title: Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase. Authors: Srivastava, S.K. / Rajasree, K. / Gopal, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 76.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3q83SC ![]() 3q89C ![]() 3q8uC ![]() 3q8vC ![]() 3q8yC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 1 - 149 / Label seq-ID: 1 - 149
|
-
Components
#1: Protein | Mass: 17663.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: genomic DNA Source: (gene. exp.) ![]() ![]() Strain: COL / Gene: ndk, SACOL1509 / Plasmid: pET22b / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.52 % |
---|---|
Crystal grow | Temperature: 298 K / Method: microbatch crystallization / pH: 5 Details: 0.1M Mgacetate, 0.1M citric acid, pH 5, 14% PEG 8000 , Microbatch Crystallization, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2010 / Details: Goebel Mirrors |
Radiation | Monochromator: CuK (Alpha) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→37.65 Å / Num. obs: 13104 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 46.4 |
Reflection shell | Resolution: 2.36→2.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 20.4 / Num. unique all: 1550 / % possible all: 78.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3Q83 Resolution: 2.38→37.65 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.553 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.665 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.239 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→37.65 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.377→2.439 Å / Total num. of bins used: 20
|