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- PDB-3pgm: THE STRUCTURE OF YEAST PHOSPHOGLYCERATE MUTASE AT 0.28 NM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 3pgm
TitleTHE STRUCTURE OF YEAST PHOSPHOGLYCERATE MUTASE AT 0.28 NM RESOLUTION
ComponentsPhosphoglycerate mutase 1
KeywordsTRANSFERASE (PHOSPHORYL)
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
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
3-PHOSPHOGLYCERIC ACID / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsCampbell, J.W. / Hodgson, G.I. / Warwicker, J. / Winn, S.I. / Watson, H.C.
Citation
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.
#1: Journal: To be Published
Title: The Amino-Acid Sequence of Yeast Phosphoglycerate Mutase
Authors: Fothergill, L.A. / Harkins, R.N.
#2: 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.
#3: Journal: Nature / Year: 1974
Title: Structure of Yeast Phosphoglycerate Mutase
Authors: Campbell, J.W. / Watson, H.C. / Hodgson, G.I.
#4: Journal: Nature New Biol. / Year: 1972
Title: Low Resolution Structure of Yeast Phosphoglycerate Mutase
Authors: Campbell, J.W. / Hodgson, G.I. / Watson, H.C.
#5: Journal: J.Mol.Biol. / Year: 1971
Title: A Preliminary X-Ray Crystallographic Investigation of Yeast Phosphoglycerate Mutase
Authors: Campbell, J.W. / Hodgson, G.I. / Watson, H.C. / Scopes, R.K.
History
DepositionApr 6, 1982Processing site: BNL
SupersessionMay 26, 1982ID: 1PGM
Revision 1.0May 26, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 14, 2013Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5May 31, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET CAUTION. THE DEFINITION OF THE BEGINNING AND END OF HELICES AND SHEET STRANDS GIVEN BELOW ...SHEET CAUTION. THE DEFINITION OF THE BEGINNING AND END OF HELICES AND SHEET STRANDS GIVEN BELOW DEPENDS SOMEWHAT ON THE CRITERIA USED TO DEFINE A *GOOD* HYDROGEN BOND. TURNS LISTED BELOW ARE THOSE WHERE CA(1)-CA(4) IS LESS THAN 5.7 ANGSTROMS AND O(1)-N(4) IS LESS THAN 3.2 ANGSTROMS. FULL TURN DEFINITION MUST AWAIT FURTHER REFINEMENT.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0948
Polymers54,3382
Non-polymers7566
Water00
1
A: Phosphoglycerate mutase 1
B: Phosphoglycerate mutase 1
hetero molecules

A: Phosphoglycerate mutase 1
B: Phosphoglycerate mutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,18916
Polymers108,6764
Non-polymers1,51312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)96.400, 85.900, 81.900
Angle α, β, γ (deg.)90.00, 120.60, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-1), (-1), (1))

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Components

#1: Protein Phosphoglycerate mutase 1


Mass: 27168.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00950, EC: 2.7.5.3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.18 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 42 0 3708

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