1PHP | pdb_00001php

STRUCTURE OF THE ADP COMPLEX OF THE 3-PHOSPHOGLYCERATE KINASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.65 ANGSTROMS

• PDB DOI: https://doi.org/10.2210/pdb1PHP/pdb

• Classification: KINASE
• Organism(s): Geobacillus stearothermophilus
• Mutation(s): No 


• Deposited: 1994-04-12 Released: 1994-06-22 
• Deposition Author(s): Davies, G.J., Watson, H.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Work: 
  0.156 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 A.

Davies, G.J., Gamblin, S.J., Littlechild, J.A., Dauter, Z., Wilson, K.S., Watson, H.C.

(1994) Acta Crystallogr D Biol Crystallogr 50: 202-209

• PubMed: 15299460 
• DOI: https://doi.org/10.1107/S0907444993011138
• Primary Citation Related Structures: 
  1PHP


• PubMed Abstract: 
  

  The structure of the ADP complex of the enzyme 3-phosphoglycerate kinase (PGK, E.C. 2.7.2.3) from Bacillus stearothermophilus NCA-1503 has been determined by the method of molecular replacement. The structure has been refined to an R factor of 0.16 for all data between 10.0 and 1.65 A resolution, using data collected on the Hendrix-Lentfer imaging plate at the EMBL outstation in Hamburg. The r.m.s. deviations from stereochemical ideality are 0.010 and 0.011 A for bonds and planes, respectively. Although crystallized in the presence of the nucleotide product MgATP, the high-resolution structure reveals the bound nucleotide to be MgADP reflecting the low intrinsic ATPase activity of PGK. Although the two domains of this enzyme are found to be some 4.5 degrees closer together than is found in the yeast and horse-muscle apo-enzyme structures, this structure represents the 'open' rather than the 'closed', catalytically competent form, of the enzyme.

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Organizational Affiliation: 
• Department of Biochemistry, School of Medical Sciences, University of Bristol, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.24 kDa 
• Atom Count: 3,670 
• Modeled Residue Count: 394 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-PHOSPHOGLYCERATE KINASE	A	394	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.2.3
UniProt
Find proteins for P18912 (Geobacillus stearothermophilus) Explore P18912  Go to UniProtKB:  P18912

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Work:  0.156 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.41	α = 90
b = 73.93	β = 99.8
c = 68.57	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-06-22 
Deposition Author(s): Davies, G.J., Watson, H.C.

Revision History  

• Version 1.0: 1994-06-22
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection, Refinement description
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations