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Yorodumi- PDB-3gw8: Crystal structure of phosphoglyceromutase from Burkholderia pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gw8 | ||||||
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Title | Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with vanadate and glycerol | ||||||
Components | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | ||||||
Keywords | ISOMERASE / SSGCID / NIAID / deCODE / UWPPG / SBRI / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase. Authors: Davies, D.R. / Staker, B.L. / Abendroth, J.A. / Edwards, T.E. / Hartley, R. / Leonard, J. / Kim, H. / Rychel, A.L. / Hewitt, S.N. / Myler, P.J. / Stewart, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gw8.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gw8.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/3gw8 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/3gw8 | HTTPS FTP |
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-Related structure data
Related structure data | 3eznSC 3fdzC 3gp3C 3gp5C 3lntC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28958.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Expressed with a non-cleavable N-terminal hexahis tag Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: gpmA, BPSL0443 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) References: UniProt: Q63XU7, UniProt: Q3JWH7*PLUS, EC: 5.4.2.1 #2: Chemical | ChemComp-VO4 / #3: Chemical | #4: Chemical | ChemComp-PG4 / #5: 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: 2.18 Å3/Da / Density % sol: 43.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Emerald Cryo Screen B-4, 100 mM MES pH 6.0, 5% PEG 1000, 10% glycerol, 30% PEG 600, 11.7 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 34058 / % possible obs: 92.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Χ2: 1.666 / Net I/σ(I): 21.975 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.89 / Num. unique all: 2972 / Χ2: 1.127 / % possible all: 80.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EZN Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.859 / SU B: 3.495 / SU ML: 0.102 / SU R Cruickshank DPI: 0.192 / SU Rfree: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.82 Å2 / Biso mean: 22.537 Å2 / Biso min: 8.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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