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- PDB-1qhf: YEAST PHOSPHOGLYCERATE MUTASE-3PG COMPLEX STRUCTURE TO 1.7 A -

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Basic information

Entry
Database: PDB / ID: 1qhf
TitleYEAST PHOSPHOGLYCERATE MUTASE-3PG COMPLEX STRUCTURE TO 1.7 A
ComponentsPROTEIN (PHOSPHOGLYCERATE MUTASE)
KeywordsTRANSFERASE / TRANSFERASE (PHOSPHORYL)
Function / homology
Function and homology information


phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / 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 / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsCrowhurst, G. / Littlechild, J. / Watson, H.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A.
Authors: Crowhurst, G.S. / Dalby, A.R. / Isupov, M.N. / Campbell, J.W. / Littlechild, J.A.
History
DepositionMay 13, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 10, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PHOSPHOGLYCERATE MUTASE)
B: PROTEIN (PHOSPHOGLYCERATE MUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5348
Polymers53,7772
Non-polymers7566
Water4,810267
1
A: PROTEIN (PHOSPHOGLYCERATE MUTASE)
B: PROTEIN (PHOSPHOGLYCERATE MUTASE)
hetero molecules

A: PROTEIN (PHOSPHOGLYCERATE MUTASE)
B: PROTEIN (PHOSPHOGLYCERATE MUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,06716
Polymers107,5554
Non-polymers1,51312
Water724
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

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Components

#1: Protein PROTEIN (PHOSPHOGLYCERATE MUTASE)


Mass: 26888.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00950, EC: 5.4.2.1
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.71 Å3/Da / Density % sol: 51.12 %
Crystal growpH: 6.8
Details: 55% AMMONIUM SULFATE IN 10MM IMIDAZOLE BUFFER PH 6.8 WITH 1MM 3PG AND CONCENTRATION OF 10 MG ML PROTEIN
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
255 %ammonium sulfate1reservoir
310 mMimidazole1reservoir
41 mM3PG substrate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.889
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.889 Å / Relative weight: 1
ReflectionResolution: 1.7→22 Å / Num. obs: 42944 / % possible obs: 82.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.088
Reflection shellResolution: 1.7→2.3 Å / % possible all: 77.2
Reflection
*PLUS
Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 77.2 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: 3PGM

3pgm


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 -5 %RANDOM
Rwork0.177 ---
obs-42944 82.5 %-
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 42 267 4107
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.84
X-RAY DIFFRACTIONp_mcangle_it3.56
X-RAY DIFFRACTIONp_scbond_it5.78
X-RAY DIFFRACTIONp_scangle_it7.710
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.150.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.220
X-RAY DIFFRACTIONp_special_tor

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