1NMO

Structural genomics, protein ybgI, unknown function


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1186/1472-6807-3-7
  • Primary Citation of Related Structures:  1LQA, 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.

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein ybgI
A, B, C, D, E, F
247Escherichia coli (strain K12)Gene Names: ybgI
Find proteins for P0AFP6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFP6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D, E, F
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 154.660α = 90.00
b = 154.660β = 90.00
c = 57.520γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
RESOLVEphasing
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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