[English] 日本語
![](img/lk-miru.gif)
- PDB-6rby: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6rby | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine derivative | ||||||
![]() | NAD kinase 1 | ||||||
![]() | TRANSFERASE / tetrameric NAD kinase | ||||||
Function / homology | ![]() NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gelin, M. / Labesse, G. | ||||||
![]() | ![]() Title: From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus. Authors: Gelin, M. / Paoletti, J. / Nahori, M.A. / Huteau, V. / Leseigneur, C. / Jouvion, G. / Dugue, L. / Clement, D. / Pons, J.L. / Assairi, L. / Pochet, S. / Labesse, G. / Dussurget, O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 119.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 806.2 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rboC ![]() 6rbpC ![]() 6rbqC ![]() 6rbrC ![]() 6rbsC ![]() 6rbtC ![]() 6rbuC ![]() 6rbvC ![]() 6rbwC ![]() 6rbxC ![]() 6rbzC ![]() 6rc0C ![]() 6rc1C ![]() 6rc2C ![]() 6rc3C ![]() 6rc4C ![]() 6rc5C ![]() 6rc6C ![]() 6rg6C ![]() 6rg7C ![]() 6rg8C ![]() 6rg9C ![]() 6rgaC ![]() 6rgbC ![]() 6rgcC ![]() 6rgdC ![]() 6rr2C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 31045.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: nadK1, lmo0968 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-JYW / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.83 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: evaporation / pH: 5 Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 4, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→48.262 Å / Num. obs: 14151 / % possible obs: 85 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/σ(I): 15 / Num. measured all: 49510 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.19 Å2 / Biso mean: 50.9221 Å2 / Biso min: 23.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.312→48.262 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|