3Q3V

Crystal structure of Phosphoglycerate Kinase from Campylobacter jejuni.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.145 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 

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.Genom. 13: 15-26

  • DOI: 10.1007/s10969-012-9131-9
  • Primary Citation of Related Structures:  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 jeju ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoglycerate kinase
A, B
403Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)Gene Names: pgk
EC: 2.7.2.3
Find proteins for Q9PMQ5 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Go to UniProtKB:  Q9PMQ5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMT
Query on FMT

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Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A, B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 = 110.280α = 90.00
b = 165.220β = 90.00
c = 54.596γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXmodel building
CCP4phasing
CCP4model building
PHENIXphasing
MrBUMPphasing
REFMACrefinement
Blu-Icedata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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