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- PDB-1bq3: SACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1bq3
TitleSACCHAROMYCES CEREVISIAE PHOSPHOGLYCERATE MUTASE IN COMPLEX WITH INOSITOL HEXAKISPHOSPHATE
ComponentsPROTEIN (PHOSPHOGLYCERATE MUTASE 1)
KeywordsISOMERASE / TRANSFERASE (PHOSPHORYL) / GLYCOLYTIC ENZYME
Function / homology
Function and homology information


phosphoglycerate mutase activity / Gluconeogenesis / Glycolysis / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Neutrophil degranulation / gluconeogenesis / glycolytic process / mitochondrial intermembrane space / mitochondrial outer membrane ...phosphoglycerate mutase activity / Gluconeogenesis / Glycolysis / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Neutrophil degranulation / 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
INOSITOL HEXAKISPHOSPHATE / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.7 Å
AuthorsRigden, D.J. / Phillips, S.E.V. / Fothergill-Gilmore, L.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Polyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis.
Authors: Rigden, D.J. / Walter, R.A. / Phillips, S.E. / Fothergill-Gilmore, L.A.
#1: 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. / Phillips, S.E.V.P. / Fothergill-Gilmore, L.A.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: The 2.3 Angstroms X-Ray Structure of S.Cerevisiae Phosphoglycerate Mutase
Authors: Rigden, D.J. / Alexeev, D. / Phillips, S.E.V.P. / Fothergill-Gilmore, L.A.
History
DepositionAug 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 14, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id ..._chem_comp.pdbx_synonyms / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: PROTEIN (PHOSPHOGLYCERATE MUTASE 1)
C: PROTEIN (PHOSPHOGLYCERATE MUTASE 1)
A: PROTEIN (PHOSPHOGLYCERATE MUTASE 1)
B: PROTEIN (PHOSPHOGLYCERATE MUTASE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,77410
Polymers110,0694
Non-polymers1,7046
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.580, 93.380, 148.560
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.00014, 0.00205), (0.00014, -1, -0.00063), (0.00205, 0.00063, -1)
Vector: -0.0048, 45.09037, 74.25165)

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Components

#1: Protein
PROTEIN (PHOSPHOGLYCERATE MUTASE 1) / PHOSPHOGLYCEROMUTASE


Mass: 27517.369 Da / Num. of mol.: 4 / 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-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Nonpolymer detailsHETEROGEN: IHP MODELLED AS SEMI-IONIZED

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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: PROTEIN WAS CRYSTALLISED FROM 22-24% PEG 4000 60MM TRIS-HCL, pH 8.65
Crystal
*PLUS
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 41238 / % possible obs: 66 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.9 / % possible all: 54.6
Reflection
*PLUS
% possible obs: 66 %
Reflection shell
*PLUS
% possible obs: 54.6 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 5PGM

5pgm


Resolution: 2.7→30 Å / Rfactor Rfree error: 0.0052 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: C-TERMINAL RESIDUES A 235 - A 246, B 236 - B 246, C 236 - C 246 AND D 235 - D 246 ARE NOT VISIBLE IN ELECTRON DENSITY MAP. CLEAVAGE OF SOME OR ALL OF THESE RESIDUES MAY HAVE OCCURRED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2139 5 %RANDOM
Rwork0.2 ---
obs0.2 41238 66 %-
Displacement parametersBiso mean: 18.1 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 92 0 7574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.09
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: 2.7→2.82 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.317 187 5 %
Rwork0.279 3949 -
obs--54.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PARAM.SO4TOP.SO4
X-RAY DIFFRACTION4IP6.PARIP6.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.09
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.317 / % reflection Rfree: 5 % / Rfactor Rwork: 0.279

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