+Open data
-Basic information
Entry | Database: PDB / ID: 3h3n | ||||||
---|---|---|---|---|---|---|---|
Title | Glycerol Kinase H232R with Glycerol | ||||||
Components | Glycerol kinase | ||||||
Keywords | TRANSFERASE / glycerol / kinase / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphoprotein | ||||||
Function / homology | Function and homology information glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Enterococcus casseliflavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Yeh, J.I. / Kettering, R.D. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation Authors: Yeh, J.I. / Kettering, R. / Saxl, R. / Bourand, A. / Darbon, E. / Joly, N. / Briozzo, P. / Deutscher, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3h3n.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3h3n.ent.gz | 165.2 KB | Display | PDB format |
PDBx/mmJSON format | 3h3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/3h3n ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h3n | HTTPS FTP |
---|
-Related structure data
Related structure data | 3d7eC 3flcC 3h3oC 3h45C 3h46C 1xupS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55831.535 Da / Num. of mol.: 2 / Mutation: H232R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: glpK / Plasmid: pOXO4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: O34153, glycerol kinase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: KH2PO4, PEG 8000, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. obs: 115245 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rsym value: 0.087 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.498 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XUP Resolution: 1.73→10 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 3 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
| ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.25 Å2 / Biso mean: 37.022 Å2 / Biso min: 18.51 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→10 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
|