Structural genomics, ybgI protein, unknown function

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal Structure of Escherichia coli Protein ybgI, a toroidal structure with a dinuclear metal site

Ladner, J.E.Obmolova, G.Teplyakov, A.Howard, A.J.Khil, P.P.Camerini-Otero, R.D.Gilliland, G.L.

(2003) BMC Struct Biol 3: 7

  • DOI: https://doi.org/10.1186/1472-6807-3-7
  • Primary Citation of Related Structures:  
    1LQA, 1NMO, 1NMP

  • PubMed Abstract: 

    The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.

  • Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA. jane.ladner@nist.gov

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein ybgI
A, B, C, D, E
A, B, C, D, E, F
247Escherichia coliEscherichia coli O157:H7
This entity is chimeric
Mutation(s): 0 
Gene Names: YBGI OR B0710 OR Z0861 OR ECS0735
Find proteins for P0AFP6 (Escherichia coli (strain K12))
Explore P0AFP6 
Go to UniProtKB:  P0AFP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFP6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
J [auth C]
K [auth C]
G [auth A],
H [auth A],
I [auth B],
J [auth C],
K [auth C],
L [auth D],
M [auth D],
N [auth E],
O [auth E],
P [auth F],
Q [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.73α = 90
b = 156.73β = 90
c = 57.61γ = 120
Software Package:
Software NamePurpose
MAR345data collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description