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Yorodumi- PDB-1bwf: ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bwf | ||||||
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Title | ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION | ||||||
Components | GLYCEROL KINASE | ||||||
Keywords | TRANSFERASE / KINASE / DOMAIN MOTION / ALLOSTERIC REGULATION HYDROLASE / LIPID DEGRADATION / PLATELET FACTOR | ||||||
Function / homology | Function and homology information glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / DNA damage response / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Bystrom, C.E. / Pettigrew, D.W. / Branchaud, B.P. / Remington, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion. Authors: Bystrom, C.E. / Pettigrew, D.W. / Branchaud, B.P. / O'Brien, P. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bwf.cif.gz | 207.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bwf.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bwf_validation.pdf.gz | 998.2 KB | Display | wwPDB validaton report |
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Full document | 1bwf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1bwf_validation.xml.gz | 54.6 KB | Display | |
Data in CIF | 1bwf_validation.cif.gz | 72.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bwf ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bwf | HTTPS FTP |
-Related structure data
Related structure data | 1gljSC 1gllC 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 56261.484 Da / Num. of mol.: 2 / Mutation: S58W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Tissue: PLATELET / Description: CLONED GENE / Organ: SEED / Gene (production host): GLPK / Production host: Escherichia coli (E. coli) / Strain (production host): DG1 (DE3) / References: UniProt: P0A6F3, glycerol kinase #2: Chemical | #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 22234 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.061 |
Reflection | *PLUS Num. obs: 24796 / Num. measured all: 84144 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GLJ Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: DUE TO LIMITED RESOLUTION OF THE DIFFRACTION DATA NO SOLVENT MOLECULES WERE ADDED TO THE STRUCTURE. ONE MAGNESIUM ATOM WAS ADDED BASED ON MANGANESE SOAKING EXPERIMENTS. RESIDUES IN ...Details: DUE TO LIMITED RESOLUTION OF THE DIFFRACTION DATA NO SOLVENT MOLECULES WERE ADDED TO THE STRUCTURE. ONE MAGNESIUM ATOM WAS ADDED BASED ON MANGANESE SOAKING EXPERIMENTS. RESIDUES IN DISALLOWED REGIONS OF THE RAMACHANDRAN PLOT ARE ASSOCIATED WITH REGIONS OF POOR ELECTRON DENSITY.
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Solvent computation | Solvent model: TNT SOLVENT MODEL / Bsol: 200 Å2 / ksol: 0.7 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 22234 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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