[English] 日本語
Yorodumi- PDB-3gp3: Crystal structure of phosphoglyceromutase from Burkholderia pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gp3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 2-phosphoserine | ||||||
Components | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | ||||||
Keywords | ISOMERASE / phosphoglyceromutase / deCODE / SBRI / NIAID / UWPPG / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gp3.cif.gz | 212.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gp3.ent.gz | 169.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gp3_validation.pdf.gz | 495.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gp3_full_validation.pdf.gz | 513.2 KB | Display | |
Data in XML | 3gp3_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 3gp3_validation.cif.gz | 64.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/3gp3 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/3gp3 | HTTPS FTP |
-Related structure data
Related structure data | 3eznC 3fdzC 3gp5C 3gw8C 3lntC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28958.844 Da / Num. of mol.: 4 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-PG4 / #3: Chemical | ChemComp-PO3 / #4: Chemical | ChemComp-SEP / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.67 % |
---|---|
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 source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
---|---|
Detector | Date: Dec 4, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 149575 / % possible obs: 95.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Χ2: 1.703 / Net I/σ(I): 18.062 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.4 / Num. unique all: 13280 / Χ2: 1.481 / % possible all: 84.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.574 / SU B: 1.939 / SU ML: 0.07 / SU R Cruickshank DPI: 0.101 / SU Rfree: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 58.79 Å2 / Biso mean: 19.203 Å2 / Biso min: 2 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.499→1.538 Å / Total num. of bins used: 20
|