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Yorodumi- PDB-3flc: Crystal structure of the His-tagged H232R mutant of glycerol kina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3flc | ||||||
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Title | Crystal structure of the His-tagged H232R mutant of glycerol kinase from Enterococcus casseliflavus with glycerol | ||||||
Components | Glycerol kinase | ||||||
Keywords | TRANSFERASE / ATP-binding / Glycerol metabolism / Kinase / 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: 1.85 Å | ||||||
Authors | Briozzo, P. | ||||||
Citation | Journal: Biochemistry / Year: 2008 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3flc.cif.gz | 215.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3flc.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 3flc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/3flc ftp://data.pdbj.org/pub/pdb/validation_reports/fl/3flc | HTTPS FTP |
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-Related structure data
Related structure data | 3d7eC 3h3nC 3h3oC 3h45C 3h46C 1r59S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57237.070 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 | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0M ammonium sulfate, 5%(v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Detector: CCD / Date: Mar 17, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 87047 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 18.25 % / Rsym value: 0.073 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.85→1.92 Å / Mean I/σ(I) obs: 2.15 / Rsym value: 0.598 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R59, molecule O Resolution: 1.85→30 Å / σ(F): 2 / Stereochemistry target values: CNS
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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