[English] 日本語

- PDB-4c5l: Structure of the pyridoxal kinase from Staphylococcus aureus in c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4c5l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the pyridoxal kinase from Staphylococcus aureus in complex with pyridoxal | ||||||
![]() | PHOSPHOMETHYLPYRIMIDINE KINASE | ||||||
![]() | TRANSFERASE / RIBOKINASE | ||||||
Function / homology | ![]() phosphomethylpyrimidine kinase activity / hydroxymethylpyrimidine kinase activity / pyridoxal kinase / thiamine biosynthetic process / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nodwell, M. / Alte, F. / Sieber, S.A. / Schneider, S. | ||||||
![]() | ![]() Title: A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage. Authors: Nodwell, M.B. / Koch, M.F. / Alte, F. / Schneider, S. / Sieber, S.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 413.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 344.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4c5jSC ![]() 4c5kC ![]() 4c5mC ![]() 4c5nC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||
2 | ![]()
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: Protein | Mass: 29811.793 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q99W31, UniProt: A0A0H3JTP0*PLUS, pyridoxal kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PXL / | #5: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | FIRST AMINO ACID IS A GLY INSTEAD OF MET DUE TO REMOVAL OF THE AFFINITY TAG | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45 % / Description: NONE |
---|---|
Crystal grow | Details: 50MM HEPES PH 7.6, 2M NH4SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.81 Å / Num. obs: 90725 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.1 / % possible all: 97 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4C5J Resolution: 1.85→43.81 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.071 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.128 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→43.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|