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Open data
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Basic information
Entry | Database: PDB / ID: 5pgm | ||||||
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Title | SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE | ||||||
![]() | PHOSPHOGLYCERATE MUTASE 1 | ||||||
![]() | ISOMERASE / TRANSFERASE (PHOSPHORYL) / GLYCOLYTIC ENZYME | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rigden, D.J. / Phillips, S.E.V. / Fothergill-Gilmore, L.A. | ||||||
![]() | ![]() Title: Sulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism. Authors: Rigden, D.J. / Walter, R.A. / Phillips, S.E. / Fothergill-Gilmore, L.A. #1: ![]() 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. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 406.8 KB | Display | ![]() |
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PDB format | ![]() | 336.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.5 KB | Display | ![]() |
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Full document | ![]() | 531.9 KB | Display | |
Data in XML | ![]() | 86.2 KB | Display | |
Data in CIF | ![]() | 123.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pgmS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, 0.00054, 0.00298), Vector: |
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Components
#1: Protein | Mass: 27517.369 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ALA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.1 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.65 / Details: pH 8.65 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Rigden, D.J., (1998) J.Mol.Biol., 276, 449. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / 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: 2.12→30 Å / Num. obs: 120182 / % possible obs: 89.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.12→2.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4 / % possible all: 80.5 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 90.8 % |
Reflection shell | *PLUS Lowest resolution: 2.2 Å / % possible obs: 81.8 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 3.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4PGM Resolution: 2.12→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze | Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.12→2.22 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.197 / Rfactor Rfree: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.2 Å / Rfactor Rfree: 0.346 / Rfactor obs: 0.307 |