1CRW

CRYSTAL STRUCTURE OF APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR AT 2.0A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.

Shen, Y.Q.Li, J.Song, S.Y.Lin, Z.J.

(2000) J.Struct.Biol. 130: 1-9

  • DOI: 10.1006/jsbi.2000.4220

  • PubMed Abstract: 
  • d-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) shows cooperative properties for binding coenzymes. The structure of apo-GAPDH from Palinurus versicolor has been solved at 2.0 A resolution by X-ray crystallography. The final model gives a crystall ...

    d-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) shows cooperative properties for binding coenzymes. The structure of apo-GAPDH from Palinurus versicolor has been solved at 2.0 A resolution by X-ray crystallography. The final model gives a crystallographic R factor of 0.178 in the resolution range 8 to 2 A. The structural comparison with holo-GAPDH from the same species reveals a conformational change induced by coenzyme binding similar to that observed in Bacillus stearothermophilus GAPDH but to a lesser extent. The differences in magnitude during the apo-holo transition between these two enzymes were analyzed with respect to the change of the amino acid composition in the coenzyme binding pocket. In the crystalline state of apo-GAPDH, the overall structures of the subunits are similar to each other; however, significant differences in temperature factors and minor differences in domain rotation upon coenzyme binding were observed for different subunits. These structural features are discussed in relation to the environmental asymmetry of crystallographically independent subunits.


    Related Citations: 
    • Structure of Holo-Glyceraldehyde-3-phosphate Dehydrogenase from Palinurus Versicolor Refined at 2A Resolution
      Song, S.,Li, J.,Lin, Z.
      (1998) Acta Crystallogr.,Sect.D 54: 558


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Academia Sinica, Beijing, 100101, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
G, R
333Panulirus versicolorEC: 1.2.1.12
Find proteins for P56649 (Panulirus versicolor)
Go to UniProtKB:  P56649
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.450α = 90.00
b = 99.840β = 115.14
c = 80.790γ = 90.00
Software Package:
Software NamePurpose
WEISdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
WEISdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation