1QHF | pdb_00001qhf

YEAST PHOSPHOGLYCERATE MUTASE-3PG COMPLEX STRUCTURE TO 1.7 A

• PDB DOI: https://doi.org/10.2210/pdb1QHF/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1999-05-13 Released: 1999-06-10 
• Deposition Author(s): Crowhurst, G., Littlechild, J., Watson, H.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor) 
• R-Value Work: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A.

Crowhurst, G.S., Dalby, A.R., Isupov, M.N., Campbell, J.W., Littlechild, J.A.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1822-1826

• PubMed: 10531478 
• DOI: https://doi.org/10.1107/s0907444999009944
• Primary Citation Related Structures: 
  1QHF


• PubMed Abstract: 
  

  The crystal structure of the tetrameric glycolytic enzyme phosphoglycerate mutase from the yeast Saccharomyces cerevisiae has been determined to 1.7 A resolution in complex with the sugar substrate. The difference map indicates that 3-phosphoglycerate is bound at the base of a 12 A cleft, positioning C2 of the substrate within 3.5 A of the primary catalytic residue, histidine 8.

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Organizational Affiliation: 
• Schools of Chemistry, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, England.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.53 kDa 
• Atom Count: 4,107 
• Modeled Residue Count: 480 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PHOSPHOGLYCERATE MUTASE)	A, B	240	Saccharomyces cerevisiae	Mutation(s): 0  EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
UniProt
Find proteins for P00950 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00950  Go to UniProtKB:  P00950

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PG	E [auth A], H [auth B]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
SO4	C [auth A], D [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor) 
• R-Value Work:  0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.4	α = 90
b = 85.9	β = 120.6
c = 81.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-10 
Deposition Author(s): Crowhurst, G., Littlechild, J., Watson, H.C.

Revision History  

• Version 1.0: 1999-06-10
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description