3SBO

Structure of E.coli GDH from native source


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.204 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization.

Totir, M.Echols, N.Nanao, M.Gee, C.L.Moskaleva, A.Gradia, S.Iavarone, A.T.Berger, J.M.May, A.P.Zubieta, C.Alber, T.

(2012) Plos One 7: e32498-e32498

  • DOI: 10.1371/journal.pone.0032498
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein cryst ...

    Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADP-specific glutamate dehydrogenase
A, B, C, D, E, F
447Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gdhA
EC: 1.4.1.4
Find proteins for P00370 (Escherichia coli (strain K12))
Go to UniProtKB:  P00370
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.204 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 101.922α = 90.00
b = 151.617β = 90.00
c = 169.970γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Structure summary
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description