+Open data
-Basic information
Entry | Database: PDB / ID: 4pgm | ||||||
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Title | SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE | ||||||
Components | PHOSPHOGLYCERATE MUTASE 1 | ||||||
Keywords | ISOMERASE / TRANSFERASE (PHOSPHORYL) / GLYCOLYTIC ENZYME | ||||||
Function / homology | Function and homology information phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rigden, D.J. / Alexeev, D. / Phillips, S.E.V. / Fothergill-Gilmore, L.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The 2.3 A X-ray crystal structure of S. cerevisiae phosphoglycerate mutase. Authors: Rigden, D.J. / Alexeev, D. / Phillips, S.E. / Fothergill-Gilmore, L.A. #1: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981 Title: Structure and Activity of Phosphoglycerate Mutase Authors: Winn, S.I. / Watson, H.C. / Harkins, R.N. / Fothergill, L.A. #2: Journal: Nature / Year: 1974 Title: Structure of Yeast Phosphoglycerate Mutase Authors: Campbell, J.W. / Watson, H.C. / Hodgson, G.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pgm.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pgm.ent.gz | 168.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pgm_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 4pgm_full_validation.pdf.gz | 474.2 KB | Display | |
Data in XML | 4pgm_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 4pgm_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/4pgm ftp://data.pdbj.org/pub/pdb/validation_reports/pg/4pgm | HTTPS FTP |
-Related structure data
Related structure data | 3pgmS S: Starting model for refinement |
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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: 27517.369 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S150 / Cell line: 293 / Cellular location: CYTOPLASM / Gene: GPM / Gene (production host): GPM / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S150-GPM\:\:HIS3 / References: UniProt: P00950, EC: 5.4.2.1 #2: 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: 2.78 Å3/Da / Density % sol: 55.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.65 Details: PROTEIN WAS CRYSTALLISED FROM 22-24% PEG 4000 60MM TRIS-HCL, PH 8.65, 120MM LI2SO4, AND 1MM INOSITOL HEXAKISPHOSPHATE | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 49635 / % possible obs: 88.7 % / Redundancy: 6.27 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 4.85 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.41 / % possible all: 89.9 |
Reflection | *PLUS Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 89.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PGM Resolution: 2.3→25 Å / Rfactor Rfree error: 0.0047 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 21.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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