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- PDB-3pgk: The structure of yeast phosphoglycerate kinase at 0.25 nm resolution -

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Entry
Database: PDB / ID: 3pgk
TitleThe structure of yeast phosphoglycerate kinase at 0.25 nm resolution
ComponentsPHOSPHOGLYCERATE KINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE(CARBOXYL AS ACCEPTOR)
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / mitochondrion / ATP binding / plasma membrane ...Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / glycolytic process / ADP binding / mitochondrion / ATP 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 / ADENOSINE-5'-TRIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsShaw, P.J. / Walker, N.P. / Watson, H.C.
Citation
#1: Journal: Biochem.J. / Year: 1983
Title: The Complete Amino Acid Sequence of Yeast Phosphoglycerate Kinase
Authors: Perkins, R.E. / Conroy, S.C. / Dunbar, B. / Fothergill, L.A. / Tuite, M.F. / Dobson, M.J. / Kingsman, S.M. / Kingsman, A.J.
#2: Journal: Embo J. / Year: 1982
Title: Sequence and Structure of Yeast Phosphoglycerate Kinase
Authors: Watson, H.C. / Walker, N.P.C. / Shaw, P.J. / Bryant, T.N. / Wendell, P.L. / Fothergill, L.A. / Perkins, R.E. / Conroy, S.C. / Dobson, M.J. / Tuite, M.F. / Kingsman, A.J. / Kingsman, S.M.
#3: Journal: Nature / Year: 1974
Title: Structure of Yeast Phosphoglycerate Kinase
Authors: Bryant, T.N. / Watson, H.C. / Wendell, P.L.
#4: Journal: Nature New Biol. / Year: 1972
Title: Low Resolution Structure of Yeast Phosphoglycerate Kinase
Authors: Wendell, P.L. / Bryant, T.N. / Watson, H.C.
#5: Journal: J.Mol.Biol. / Year: 1971
Title: Crystallographic Study of Yeast Phosphoglycerate Kinase
Authors: Watson, H.C. / Wendell, P.L. / Scopes, R.K.
History
DepositionJul 15, 1982Processing site: BNL
SupersessionSep 24, 1982ID: 1PGK
Revision 1.0Sep 24, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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:
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Assembly

Deposited unit
A: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3704
Polymers44,6521
Non-polymers7183
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.600, 54.400, 93.000
Angle α, β, γ (deg.)90.00, 134.40, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THIS ATOM MAY BE MAGNESIUM OR MANGANESE.

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Components

#1: Protein PHOSPHOGLYCERATE KINASE


Mass: 44652.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00560, phosphoglycerate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / 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: 2.56 Å3/Da / Density % sol: 51.97 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 43 0 3191

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