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- PDB-1fzt: SOLUTION STRUCTURE AND DYNAMICS OF AN OPEN B-SHEET, GLYCOLYTIC EN... -

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Entry
Database: PDB / ID: 1fzt
TitleSOLUTION STRUCTURE AND DYNAMICS OF AN OPEN B-SHEET, GLYCOLYTIC ENZYME-MONOMERIC 23.7 KDA PHOSPHOGLYCERATE MUTASE FROM SCHIZOSACCHAROMYCES POMBE
ComponentsPHOSPHOGLYCERATE MUTASE
KeywordsISOMERASE / open B-sheet-helices
Function / homology
Function and homology information


Glycolysis / Gluconeogenesis / Neutrophil degranulation / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / canonical glycolysis / gluconeogenesis / nucleus / 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
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsUhrinova, S. / Uhrin, D. / Nairn, J. / Price, N.C. / Fothergill-Gilmore, L.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution structure and dynamics of an open beta-sheet, glycolytic enzyme, monomeric 23.7 kDa phosphoglycerate mutase from Schizosaccharomyces pombe.
Authors: Uhrinova, S. / Uhrin, D. / Nairn, J. / Price, N.C. / Fothergill-Gilmore, L.A. / Barlow, P.N.
#1: Journal: J.Biomol.NMR / Year: 1997
Title: Backbone Assignment of Double Labelled 23.7 kDa Phosphoglycerate Mutase from Scizosaccharomyces pombe
Authors: Uhrinova, S. / Uhrin, D. / Nairn, J. / Price, N.C. / Fothergill-Gilmore, L.A. / BARLOW, P.N.
#2: Journal: J.MAGN.RESON. / Year: 2000
Title: 3D HCCH3-TOCSY for Resonance Assignment of Methyl-containing Side Chains in (13)C-labeled Proteins
Authors: Uhrin, D. / Uhrinova, S. / Leadbeater, C. / Nairn, J. / Price, N.C. / BARLOW, P.N.
History
DepositionOct 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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


Theoretical massNumber of molelcules
Total (without water)23,8001
Polymers23,8001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 55structures with the lowest energy
RepresentativeModel #21lowest energy

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Components

#1: Protein PHOSPHOGLYCERATE MUTASE


Mass: 23800.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: PMA91 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36623, EC: 5.4.2.1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 1mM phosphoglycerate mutase; 200mM sodium acetate, 200mM ammonium sulphate; 90% H2O, 10% D2O.
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian AMXVarianAMX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
FelixFelix95Biosym Technologiesprocessing
XEASYXEASY(1995)Bartels et al.data analysis
X-PLOR3.851Brungerrefinement
model-freeextended model, 1995Mandel et al.data analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: structures are based om 3125 noe restraints, 74 hydrogen bonds, and 149 torsion angles
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 55 / Conformers submitted total number: 21

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