[English] 日本語
![](img/lk-miru.gif)
- PDB-5zwb: Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typh... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5zwb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via a Schiff base | |||||||||
![]() | (Pyridoxine/pyridoxal/pyridoxamine ...) x 2 | |||||||||
![]() | TRANSFERASE / Pyridoxal kinase / Schiff base linked- Pyridoxal / Salmonella typhimurium | |||||||||
Function / homology | ![]() hydroxymethylpyrimidine kinase activity / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / magnesium ion binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Deka, G. / Benazir, J.F. / Kalyani, J.N. / Savithri, H.S. / Murthy, M.R.N. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and functional studies on Salmonella typhimurium pyridoxal kinase: the first structural evidence for the formation of Schiff base with the substrate. Authors: Deka, G. / Kalyani, J.N. / Jahangir, F.B. / Sabharwal, P. / Savithri, H.S. / Murthy, M.R.N. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 97.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 812.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 814.9 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zw9C ![]() 5zwaC ![]() 2ddmS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Pyridoxine/pyridoxal/pyridoxamine ... , 2 types, 2 molecules AB
#1: Protein | Mass: 32287.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0M0PWM4, UniProt: A0A0F7J8S0*PLUS, pyridoxal kinase |
---|---|
#2: Protein | Mass: 32215.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0M0PWM4, UniProt: A0A0F7J8S0*PLUS, pyridoxal kinase |
-Non-polymers , 6 types, 349 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 51.77 % |
---|---|
Crystal grow | Temperature: 293 K / Method: batch mode / pH: 8.5 / Details: 50% PEG 4000, 10% Glycerol, 100mM Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.94 Å / Num. obs: 36036 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.03 / Rrim(I) all: 0.12 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 5152 / Rpim(I) all: 0.11 / Rrim(I) all: 0.46 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2DDM Resolution: 2.2→39.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.499 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.198 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.055 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→39.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|