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- PDB-1qpg: 3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q -

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Basic information

Entry
Database: PDB / ID: 1qpg
Title3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q
Components3-PHOSPHOGLYCERATE KINASE
KeywordsPHOSPHOTRANSFERASE (CARBOXYL ACCEPTOR) / KINASE / ACETYLATION / GLYCOLYSIS
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / mitochondrion / ATP binding / metal ion binding ...Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMcphillips, T.M. / Hsu, B.T. / Sherman, M.A. / Mas, M.T. / Rees, D.C.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate.
Authors: McPhillips, T.M. / Hsu, B.T. / Sherman, M.A. / Mas, M.T. / Rees, D.C.
#1: Journal: Protein Sci. / Year: 1992
Title: Characterization of the Structure and Properties of the His 62-->Ala and Arg 38-->Ala Mutants of Yeast Phosphoglycerate Kinase: An Investigation of the Catalytic and Activatory Sites by Site- ...Title: Characterization of the Structure and Properties of the His 62-->Ala and Arg 38-->Ala Mutants of Yeast Phosphoglycerate Kinase: An Investigation of the Catalytic and Activatory Sites by Site-Directed Mutagenesis and NMR
Authors: Sherman, M.A. / Fairbrother, W.J. / Mas, M.T.
#2: Journal: Protein Eng. / Year: 1991
Title: Site-Directed Mutations of Arginine 65 at the Periphery of the Active Site Cleft of Yeast 3-Phosphoglycerate Kinase Enhance the Catalytic Activity and Eliminate Anion-Dependent Activation
Authors: Sherman, M.A. / Dean, S.A. / Mathiowetz, A.M. / Mas, M.T.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: Probing the Role of Arginines and Histidines in the Catalytic Function and Activation of Yeast 3-Phosphoglycerate Kinase by Site-Directed Mutagenesis
Authors: Sherman, M.A. / Szpikowska, B.K. / Dean, S.A. / Mathiowetz, A.M. / Mcqueen, N.L. / Mas, M.T.
History
DepositionJan 4, 1996Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 1.6Feb 14, 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: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3573
Polymers44,6411
Non-polymers7162
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.000, 70.100, 82.300
Angle α, β, γ (deg.)90.00, 122.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-PHOSPHOGLYCERATE KINASE / PGK


Mass: 44641.059 Da / Num. of mol.: 1 / Mutation: R65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: YEP9T-PGK / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): PGK-XSB44-35D / References: UniProt: P00560, phosphoglycerate kinase
#2: Chemical ChemComp-MAP / MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE


Mass: 529.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16MgN6O12P3
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlR65Q PGK1drop
210 mM5'-adenylylimidodiphosphate1drop
410 mMD-(-)-3-phosphoglycerate1drop
621 %PEG80001reservoir
720 mMmagnesium acetate1reservoir
80.02 %1reservoirNaN3
950 mMHEPES1reservoir
3tetralithium salt (AMP-PNP)1drop
5disodium salt (3-PG)1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 30, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→40.7 Å / Num. obs: 16281 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Num. measured all: 100828

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
TNTrefinement
X-PLOR3.1model building
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.4→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 13387 78.3 %
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 43 82 3271
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_deg1.781
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.67
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.262
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.67
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.262

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