Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.35 kDa 
• Atom Count: 2763 
• Modelled Residue Count: 312 
• Deposited Residue Count: 354 
• Unique protein chains: 1

3K6V

M. acetivorans Molybdate-Binding Protein (ModA) in Citrate-Bound Open Form

• PDB DOI: 10.2210/pdb3K6V/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Methanosarcina acetivorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-09 Released: 2010-01-12 
• Deposition Author(s): Chan, S., Giuroiu, I., Chernishof, I., Sawaya, M.R., Chiang, J., Gunsalus, R.P., Arbing, M.A., Perry, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.211 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

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

• PubMed: 20208152 
• DOI: 10.1107/S1744309109055158
• Primary Citation of Related Structures:  
  3K6U, 3K6V, 3K6W, 3K6X


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute-binding protein MA_0280	A	354	Methanosarcina acetivorans	Mutation(s): 0  Gene Names: MA0280, MA_0280
UniProt
Find proteins for Q8TTZ5 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8TTZ5  Go to UniProtKB:  Q8TTZ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.211 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.629	α = 90
b = 81.629	β = 90
c = 104.636	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-09 
• Released Date: 2010-01-12 
Deposition Author(s): Chan, S., Giuroiu, I., Chernishof, I., Sawaya, M.R., Chiang, J., Gunsalus, R.P., Arbing, M.A., Perry, L.J.

Revision History  

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