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- PDB-4pgm: SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE -

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Basic information

Entry
Database: PDB / ID: 4pgm
TitleSACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE
ComponentsPHOSPHOGLYCERATE MUTASE 1
KeywordsISOMERASE / TRANSFERASE (PHOSPHORYL) / GLYCOLYTIC ENZYME
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / glycolytic process / gluconeogenesis / mitochondrial intermembrane space / mitochondrial outer membrane / mitochondrion / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRigden, 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
DepositionApr 25, 1997Processing site: BNL
Revision 1.0Oct 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOGLYCERATE MUTASE 1
B: PHOSPHOGLYCERATE MUTASE 1
C: PHOSPHOGLYCERATE MUTASE 1
D: PHOSPHOGLYCERATE MUTASE 1


Theoretical massNumber of molelcules
Total (without water)110,0694
Polymers110,0694
Non-polymers00
Water14,898827
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.467, 84.555, 88.884
Angle α, β, γ (deg.)90.00, 111.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.32962, 0.02344, -0.94382), (-0.00939, -0.99956, -0.0281), (-0.94407, 0.01812, -0.32925)27.54222, 0.91271, 38.7408
2given(-0.99972, -0.02181, 0.00908), (-0.02181, 0.99976, -0.00046), (-0.00906, -0.00065, -0.99996)24.16668, 0.24496, 41.46565
3given(-0.33126, -0.01332, 0.94345), (0.01802, -0.99981, -0.00779), (0.94337, 0.01443, 0.33143)-3.2862, 0.20014, 2.26382

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Components

#1: Protein
PHOSPHOGLYCERATE MUTASE 1


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 / water


Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.5 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21 mMinositol hexakisphosphate1drop
360 mMTris-HCl1reservoirpH8.65
4120 mMlithium sulfate1reservoir
522-24 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PGM

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
RfactorNum. reflection% reflectionSelection details
Rfree0.286 3645 10 %RANDOM
Rwork0.192 ---
obs0.192 36485 88.7 %-
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.3163 Å20 Å22.6628 Å2
2---1.6434 Å20 Å2
3---1.3271 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 25 Å
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 0 827 9153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.113
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.52
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.492
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2852 298 10.1 %
Rwork0.1927 2661 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.524
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.492

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