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Yorodumi- PDB-3gp5: Crystal structure of phosphoglyceromutase from Burkholderia pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gp5 | ||||||
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Title | Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 3-phosphoglyceric acid and vanadate | ||||||
Components | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | ||||||
Keywords | ISOMERASE / phosphoglyceromutase / deCODE / UWPPG. SBRI / NIAID / SSGCID / 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: 2.25 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 | 3gp5.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gp5.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gp5_validation.pdf.gz | 781.6 KB | Display | wwPDB validaton report |
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Full document | 3gp5_full_validation.pdf.gz | 786.3 KB | Display | |
Data in XML | 3gp5_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 3gp5_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/3gp5 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/3gp5 | HTTPS FTP |
-Related structure data
Related structure data | 3eznC 3fdzC 3gp3C 3gw8C 3lntC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28958.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Expressed with an N-terminal non-cleavable 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 |
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-Non-polymers , 5 types, 232 molecules
#2: Chemical | ChemComp-PG6 / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.18 Å3/Da / Density % sol: 43.53 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Emerald Cryo B-4, 100MM MES PH 7.5, 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 MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 24, 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: 2.25→50 Å / Num. obs: 21960 / % possible obs: 94.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.068 / Χ2: 1.318 / Net I/σ(I): 13.141 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.452 / Num. unique all: 1899 / Χ2: 1.178 / % possible all: 82.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.838 / SU B: 5.868 / SU ML: 0.148 / SU R Cruickshank DPI: 0.377 / SU Rfree: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.241 / 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: 57.02 Å2 / Biso mean: 22.897 Å2 / Biso min: 3.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.246→2.304 Å / Total num. of bins used: 20
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