+Open data
-Basic information
Entry | Database: PDB / ID: 5wat | ||||||
---|---|---|---|---|---|---|---|
Title | Corynebacterium glutamicum Full length Homoserine kinase | ||||||
Components | Homoserine kinase | ||||||
Keywords | TRANSFERASE / Corynebacterium glutamicum / Homoserine Kinase / L-threonine / L-homoserine / Magnesium | ||||||
Function / homology | Function and homology information homoserine kinase / homoserine kinase activity / threonine biosynthetic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.141 Å | ||||||
Authors | Petit, C. / Ronning, D.R. | ||||||
Citation | Journal: ACS Omega / Year: 2018 Title: Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) ofCorynebacterium glutamicumEnhances l-Threonine Biosynthesis. Authors: Petit, C. / Kim, Y. / Lee, S.K. / Brown, J. / Larsen, E. / Ronning, D.R. / Suh, J.W. / Kang, C.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wat.cif.gz | 136.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wat.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/5wat ftp://data.pdbj.org/pub/pdb/validation_reports/wa/5wat | HTTPS FTP |
---|
-Related structure data
Related structure data | 5wasC 4rpfS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33478.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: thrB, Cgl1184, cg1338 / Production host: Escherichia coli (E. coli) / References: UniProt: P07128, homoserine kinase |
---|
-Non-polymers , 5 types, 211 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.99 % / Description: Diamond shaped |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: protein in 20 mM Tris pH 7.5, 150 mM NaCl, 50 mM KCl and 50 mM MgCl2 well solution: 0.25 M ammonium sulfate, 25 % PEG 3,350 and 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.141→50 Å / Num. obs: 48115 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.141→42.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4566 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4rpf Resolution: 2.141→42.335 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.7 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.141→42.335 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|