3Q3V

Crystal structure of Phosphoglycerate Kinase from Campylobacter jejuni.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni.

Zheng, H.Filippova, E.V.Tkaczuk, K.L.Dworzynski, P.Chruszcz, M.Porebski, P.J.Wawrzak, Z.Onopriyenko, O.Kudritska, M.Grimshaw, S.Savchenko, A.Anderson, W.F.Minor, W.

(2012) J Struct Funct Genomics 13: 15-26

  • DOI: https://doi.org/10.1007/s10969-012-9131-9
  • Primary Citation of Related Structures:  
    3Q3V, 3UWD

  • PubMed Abstract: 

    Phosphoglycerate kinase (PGK) is indispensable during glycolysis for anaerobic glucose degradation and energy generation. Here we present comprehensive structure analysis of two putative PGKs from Bacillus anthracis str. Sterne and Campylobacter jejuni in the context of their structural homologs. They are the first PGKs from pathogenic bacteria reported in the Protein Data Bank. The crystal structure of PGK from Bacillus anthracis str. Sterne (BaPGK) has been determined at 1.68 Å while the structure of PGK from Campylobacter jejuni (CjPGK) has been determined at 2.14 Å resolution. The proteins' monomers are composed of two domains, each containing a Rossmann fold, hinged together by a helix which can be used to adjust the relative position between two domains. It is also shown that apo-forms of both BaPGK and CjPGK adopt open conformations as compared to the substrate and ATP bound forms of PGK from other species.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate kinase
A, B
403Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819Mutation(s): 0 
Gene Names: Cj1402cpgk
EC: 2.7.2.3
UniProt
Find proteins for Q9PMQ5 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Explore Q9PMQ5 
Go to UniProtKB:  Q9PMQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PMQ5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
K [auth B],
L [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.28α = 90
b = 165.22β = 90
c = 54.596γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
CCP4model building
MrBUMPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-09
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description