1KQ3

CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

Lesley, S.A.Kuhn, P.Godzik, A.Deacon, A.M.Mathews, I.Kreusch, A.Spraggon, G.Klock, H.E.McMullan, D.Shin, T.Vincent, J.Robb, A.Brinen, L.S.Miller, M.D.McPhillips, T.M.Miller, M.A.Scheibe, D.Canaves, J.M.Guda, C.Jaroszewski, L.Selby, T.L.Elsliger, M.-A.Wooley, J.Taylor, S.S.Hodgson, K.O.Wilson, I.A.Schultz, P.G.Stevens, R.C.

(2002) Proc.Natl.Acad.Sci.USA 99: 11664-11669

  • DOI: 10.1073/pnas.142413399
  • Primary Citation of Related Structures:  1KQ4

  • PubMed Abstract: 
  • Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We descr ...

    Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.


    Organizational Affiliation

    Joint Center for Structural Genomics, Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA. lesley@gnf.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glycerol dehydrogenase
A
376Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: gldA
EC: 1.1.1.6
Find proteins for Q9WYQ4 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WYQ4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.173 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.730α = 90.00
b = 105.730β = 90.00
c = 135.790γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
RESOLVEphasing
RESOLVEmodel building
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    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: 2017-02-01
    Type: Structure summary
  • Version 1.4: 2017-10-11
    Type: Refinement description