6GWV | pdb_00006gwv

Molybdenum storage protein without polymolybdate clusters and ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.259 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6GWV

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The Molybdenum Storage Protein: A soluble ATP hydrolysis-dependent molybdate pump.

Poppe, J.Brunle, S.Hail, R.Wiesemann, K.Schneider, K.Ermler, U.

(2018) FEBS J 285: 4602-4616

  • DOI: https://doi.org/10.1111/febs.14684
  • Primary Citation Related Structures: 
    6GU5, 6GUJ, 6GWV, 6GX4

  • PubMed Abstract: 

    A continuous FeMo cofactor supply for nitrogenase maturation is ensured in Azotobacter vinelandii by developing a cage-like molybdenum storage protein (MoSto) capable to store ca. 120 molybdate molecules ( MoO 4 2 - ) as discrete polyoxometalate (POM) clusters. To gain mechanistic insight into this process, MoSto was characterized by Mo and ATP/ADP content, structural, and kinetic analysis. We defined three functionally relevant states specified by the presence of both ATP/ADP and POM clusters (MoSto funct ), of only ATP/ADP (MoSto basal ) and of neither ATP/ADP nor POM clusters (MoSto zero ), respectively. POM clusters are only produced when ATP is hydrolyzed to ADP and phosphate. V max was ca. 13 μmol phosphate ·min -1 ·mg -1 and K m for molybdate and ATP/Mg 2+ in the low micromolar range. ATP hydrolysis presumably proceeds at subunit α, inferred from a highly occupied α-ATP/Mg 2+ and a weaker occupied β-ATP/no Mg 2+ -binding site found in the MoSto funct structure. Several findings indicate that POM cluster storage is separated into a rapid ATP hydrolysis-dependent molybdate transport across the protein cage wall and a slow molybdate assembly induced by combined auto-catalytic and protein-driven processes. The cage interior, the location of the POM cluster depot, is locked in all three states and thus not rapidly accessible for molybdate from the outside. Based on V max , the entire Mo storage process should be completed in less than 10 s but requires, according to the molybdate content analysis, ca. 15 min. Long-time incubation of MoSto basal with nonphysiological high molybdate amounts implicates an equilibrium in and outside the cage and POM cluster self-formation without ATP hydrolysis. DATABASES: The crystal structures MoSto in the MoSto-F6, MoSto-F7, MoSto basal , MoSto zero , and MoSto-F1 vitro states were deposited to PDB under the accession numbers PDB 6GU5, 6GUJ, 6GWB, 6GWV, and 6GX4.


  • Organizational Affiliation
    • Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 519.45 kDa 
  • Atom Count: 34,318 
  • Modeled Residue Count: 4,608 
  • Deposited Residue Count: 4,896 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit beta269Azotobacter vinelandii DJMutation(s): 0 
UniProt
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84253 
Go to UniProtKB:  P84253
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84253
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit alpha275Azotobacter vinelandii DJMutation(s): 0 
UniProt
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84308 
Go to UniProtKB:  P84308
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84308
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
CA [auth P],
T [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth M]
DA [auth Q]
EA [auth R]
S [auth B]
U [auth D]
AA [auth M],
DA [auth Q],
EA [auth R],
S [auth B],
U [auth D],
V [auth E],
W [auth F],
X [auth G],
Y [auth N],
Z [auth N]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth M]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.259 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.71α = 90
b = 147.3β = 107.62
c = 192.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references