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- PDB-5pgm: SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE -

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Basic information

Entry
Database: PDB / ID: 5pgm
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
ALANINE / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsRigden, D.J. / Phillips, S.E.V. / Fothergill-Gilmore, L.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
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: 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.
#2: Journal: Nature / Year: 1974
Title: Structure of Yeast Phosphoglycerate Mutase
Authors: Campbell, J.W. / Watson, H.C. / Hodgson, G.I.
History
DepositionAug 19, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: 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: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: PHOSPHOGLYCERATE MUTASE 1
C: PHOSPHOGLYCERATE MUTASE 1
A: PHOSPHOGLYCERATE MUTASE 1
B: PHOSPHOGLYCERATE MUTASE 1
E: PHOSPHOGLYCERATE MUTASE 1
F: PHOSPHOGLYCERATE MUTASE 1
G: PHOSPHOGLYCERATE MUTASE 1
H: PHOSPHOGLYCERATE MUTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,76525
Polymers220,1398
Non-polymers1,62617
Water29,5091638
1
D: PHOSPHOGLYCERATE MUTASE 1
C: PHOSPHOGLYCERATE MUTASE 1
A: PHOSPHOGLYCERATE MUTASE 1
B: PHOSPHOGLYCERATE MUTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,83812
Polymers110,0694
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: PHOSPHOGLYCERATE MUTASE 1
F: PHOSPHOGLYCERATE MUTASE 1
G: PHOSPHOGLYCERATE MUTASE 1
H: PHOSPHOGLYCERATE MUTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,92713
Polymers110,0694
Non-polymers8589
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.497, 93.262, 147.329
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.00054, 0.00298), (0.00054, -1, -0.00035), (0.00298, 0.00035, -1)
Vector: -0.05664, -48.36717, 73.63743)

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Components

#1: Protein
PHOSPHOGLYCERATE MUTASE 1 / PHOSPHOGLYCEROMUTASE


Mass: 27517.369 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: S150-GPM\:\:HIS3 / References: UniProt: P00950, EC: 5.4.2.1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1638 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.89 Å3/Da / Density % sol: 57.1 %
Crystal growpH: 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
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: SRS / Beamline: PX9.5 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.12→30 Å / Num. obs: 120182 / % possible obs: 89.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.3
Reflection shellResolution: 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

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PGM

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
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5659 5 %RANDOM
Rwork0.196 ---
obs0.196 113189 89.5 %-
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å20 Å2-0.7222 Å2
2---5.1 Å20 Å2
3---2.33 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2.12→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7487 0 40 819 8346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.76
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: CONSTRAINTS
LS refinement shellResolution: 2.12→2.22 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.331 654 5 %
Rwork0.297 11656 -
obs--78.29 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PARAM.SO4TOP.SO4
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197 / Rfactor Rfree: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.76
LS refinement shell
*PLUS
Lowest resolution: 2.2 Å / Rfactor Rfree: 0.346 / Rfactor obs: 0.307

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