1MKZ | pdb_00001mkz

Crystal structure of MoaB protein at 1.6 A resolution.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.219 (Depositor) 
  • R-Value Work: 
    0.183 (Depositor) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis.

Sanishvili, R., Beasley, S., Skarina, T., Glesne, D., Joachimiak, A., Edwards, A., Savchenko, A.

(2004) J Biological Chem 279: 42139-42146

  • DOI: https://doi.org/10.1074/jbc.M407694200
  • Primary Citation of Related Structures:  
    1MKZ

  • PubMed Abstract: 

    The crystal structure of Escherichia coli MoaB was determined by multiwavelength anomalous diffraction phasing and refined at 1.6-A resolution. The molecule displayed a modified Rossman fold. MoaB is assembled into a hexamer composed of two trimers. The monomers have high structural similarity with two proteins, MogA and MoeA, from the molybdenum cofactor synthesis pathway in E. coli, as well as with domains of mammalian gephyrin and plant Cnx1, which are also involved in molybdopterin synthesis. Structural comparison between these proteins and the amino acid conservation patterns revealed a putative active site in MoaB. The structural analysis of this site allowed to advance several hypothesis that can be tested in further studies.

    • Organizational Affiliation: 

    Biosciences, Structural Biology Center, Midwest Center for Sructural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Molybdenum cofactor biosynthesis protein B
A, B
172Escherichia coliMutation(s): 3 
Gene Names: MoaB
UniProt
Find proteins for P0AEZ9 (Escherichia coli (strain K12))
Explore P0AEZ9 
Go to UniProtKB:  P0AEZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEZ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACY
Query on ACY
Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
L [auth B]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.219 (Depositor) 
  • R-Value Work:  0.183 (Depositor) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.169α = 90
b = 69.169β = 90
c = 126.184γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CNSrefinement
WARPmodel building
d*TREKdata scaling
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
ARP/wARPmodel building

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.6: 2024-11-06
    Changes: Structure summary