3K6X

M. acetivorans Molybdate-Binding Protein (ModA) in Molybdate-Bound Close Form with 2 Molecules in Asymmetric Unit Forming Beta Barrel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans

Chan, S.Giuroiu, I.Chernishof, I.Sawaya, M.R.Chiang, J.Gunsalus, R.P.Arbing, M.A.Perry, L.J.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 242-250

  • DOI: 10.1107/S1744309109055158
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the M ...

    The trace-element oxyanion molybdate, which is required for the growth of many bacterial and archaeal species, is transported into the cell by an ATP-binding cassette (ABC) transporter superfamily uptake system called ModABC. ModABC consists of the ModA periplasmic solute-binding protein, the integral membrane-transport protein ModB and the ATP-binding and hydrolysis cassette protein ModC. In this study, X-ray crystal structures of ModA from the archaeon Methanosarcina acetivorans (MaModA) have been determined in the apoprotein conformation at 1.95 and 1.69 A resolution and in the molybdate-bound conformation at 2.25 and 2.45 A resolution. The overall domain structure of MaModA is similar to other ModA proteins in that it has a bilobal structure in which two mixed alpha/beta domains are linked by a hinge region. The apo MaModA is the first unliganded archaeal ModA structure to be determined: it exhibits a deep cleft between the two domains and confirms that upon binding ligand one domain is rotated towards the other by a hinge-bending motion, which is consistent with the 'Venus flytrap' model seen for bacterial-type periplasmic binding proteins. In contrast to the bacterial ModA structures, which have tetrahedral coordination of their metal substrates, molybdate-bound MaModA employs octahedral coordination of its substrate like other archaeal ModA proteins.


    Organizational Affiliation

    UCLA-DOE Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, CA 90095, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Solute-binding protein MA_0280
A, B
354Methanosarcina acetivoransMutation(s): 0 
Gene Names: MA0280MA_0280
Find proteins for Q8TTZ5 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Go to UniProtKB:  Q8TTZ5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MOO
Query on MOO

Download CCD File 
A, B
MOLYBDATE ION
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.195α = 90
b = 65.587β = 123.95
c = 94.768γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description