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Yorodumi- PDB-1o08: Structure of Pentavalent Phosphorous Intermediate of an Enzyme Ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o08 | |||||||||
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Title | Structure of Pentavalent Phosphorous Intermediate of an Enzyme Catalyzed Phosphoryl transfer Reaction observed on cocrystallization with Glucose 1-phosphate | |||||||||
Components | beta-phosphoglucomutase | |||||||||
Keywords | ISOMERASE / Haloacid dehalogenase superfamily / phosphotransferase / pentavalent phosphate intermediate | |||||||||
Function / homology | Function and homology information beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.2 Å | |||||||||
Authors | Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. | |||||||||
Citation | Journal: Science / Year: 2003 Title: The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction. Authors: Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o08.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o08.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 1o08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/1o08 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/1o08 | HTTPS FTP |
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-Related 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: 24239.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P71447, beta-phosphoglucomutase |
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#2: Sugar | ChemComp-G16 / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 26.66 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 16% PEG 3350, 0.1M Ammonium Fluoride, 4mM b-D-Glucose-1-phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2002 / Details: mirrors |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→100 Å / Num. obs: 56998 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 8.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.045 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 15.7 / Rsym value: 0.08 / % possible all: 54.4 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. obs: 66304 / Num. measured all: 699466 |
Reflection shell | *PLUS Highest resolution: 1.2 Å / % possible obs: 54.4 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 12.4 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: SeMeth MAD model of the same protein to 1.7 angstrom Resolution: 1.2→10 Å / Num. parameters: 19983 / Num. restraintsaints: 20651 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2%
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2205
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Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor all: 0.141 / Rfactor Rfree: 0.179 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 1.22 Å |