3N6Q

Crystal structure of YghZ from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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:  
    2XHY, 3NBU, 3N6Q, 3SBO

  • 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 crystallography applications ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YghZ aldo-keto reductaseA, B, C, D, E, F, G, H346Escherichia coli DH5[alpha]Mutation(s): 0 
EC: 1.1.1
Find proteins for Q46851 (Escherichia coli (strain K12))
Explore Q46851 
Go to UniProtKB:  Q46851
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A] , J [auth B] , K [auth C] , L [auth D] , M [auth D] , N [auth E] , O [auth F] , P [auth G] , 
I [auth A],  J [auth B],  K [auth C],  L [auth D],  M [auth D],  N [auth E],  O [auth F],  P [auth G],  Q [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.7α = 90.27
b = 98.056β = 92.97
c = 98.257γ = 106.12
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references