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Yorodumi- PDB-3d7e: Enterococcus casseliflavus glycerol kinase mutant HIS232ALA compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d7e | ||||||
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Title | Enterococcus casseliflavus glycerol kinase mutant HIS232ALA complexed with glycerol | ||||||
Components | Glycerol kinase | ||||||
Keywords | TRANSFERASE / KINASE / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphoprotein | ||||||
Function / homology | Function and homology information glycerol-3-phosphate biosynthetic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / triglyceride metabolic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Enterococcus casseliflavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Yeh, J.I. / Vahedi-Faridi, A. | ||||||
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. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2005 Title: The effects of flash-annealing on glycerol kinase crystals Authors: Vahedi-Faridi, A. / Stojanoff, V. / Yeh, J.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d7e.cif.gz | 207.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d7e.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 3d7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d7e_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 3d7e_full_validation.pdf.gz | 494.7 KB | Display | |
Data in XML | 3d7e_validation.xml.gz | 43 KB | Display | |
Data in CIF | 3d7e_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d7e ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d7e | HTTPS FTP |
-Related structure data
Related structure data | 3flcC 3h3nC 3h3oC 3h45C 3h46C 1xupS 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: 55614.223 Da / Num. of mol.: 2 / Mutation: H232A 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: 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: 2.42 Å3/Da / Density % sol: 49.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 29% PEG400, 0.1M sodium acetate, 0.1M calcium acetate, 10% glycerol, PH4.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.033 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 63332 / % possible obs: 89 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.03→2.1 Å / Rmerge(I) obs: 0.261 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XUP Resolution: 2.03→39.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.906 / SU B: 2.572 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.812 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→39.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.027→2.08 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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