1RTY

Crystal Structure of Bacillus subtilis YvqK, a putative ATP-binding Cobalamin Adenosyltransferase, The North East Structural Genomics Target SR128


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional insights from structural genomics.

Forouhar, F.Kuzin, A.Seetharaman, J.Lee, I.Zhou, W.Abashidze, M.Chen, Y.Yong, W.Janjua, H.Fang, Y.Wang, D.Cunningham, K.Xiao, R.Acton, T.B.Pichersky, E.Klessig, D.F.Porter, C.W.Montelione, G.T.Tong, L.

(2007) J.STRUCT.FUNCT.GENOM. 8: 37-44

  • DOI: 10.1007/s10969-007-9018-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been character ...

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF_0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP_1951), and a 12-stranded beta-barrel with a novel fold (V. parahaemolyticus VPA1032).


    Organizational Affiliation

    Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
yvqk protein
A, B, C
193Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yvqK
EC: 2.5.1.17
Find proteins for O34899 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34899
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 104.350α = 90.00
b = 104.350β = 90.00
c = 55.985γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
COMOphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance