4NDP

Crystal structure Molybdenum Storage Protein with fully Mo-loaded cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural diversity of polyoxomolybdate clusters along the three-fold axis of the molybdenum storage protein.

Poppe, J.Warkentin, E.Demmer, U.Kowalewski, B.Dierks, T.Schneider, K.Ermler, U.

(2014) J Inorg Biochem 138: 122-128

  • DOI: 10.1016/j.jinorgbio.2014.05.009
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The molybdenum storage protein (MoSto) can store more than 100 Mo or W atoms as discrete polyoxometalate (POM) clusters. Here, we describe the three POM cluster sites along the threefold axis of the protein complex based on four X-ray structures with ...

    The molybdenum storage protein (MoSto) can store more than 100 Mo or W atoms as discrete polyoxometalate (POM) clusters. Here, we describe the three POM cluster sites along the threefold axis of the protein complex based on four X-ray structures with slightly different polyoxomolybdate compositions between 1.35 and 2 Å resolution. In contrast to the Moα-out binding site occupied by an Mo3 cluster, the Moα-in and Moβ binding sites contain rather weak and non-uniform electron density for the Mo atoms (but clearly identifiable by anomalous data), suggesting the presence of POM cluster ensembles and/or degradation products of larger aggregates. The "Moα-in cluster ensemble" was interpreted as an antiprism-like Mo6 species superimposed with an Mo7 pyramide and the "Moβ cluster ensemble" as an Mo13 cluster (present mostly in a degraded form) composed of a pyramidal Mo7 and a Mo3 building block linked by three spatially separated MoOx units. Inside the ball-shaped Mo13 cluster sits an occluded central atom, perhaps a metal ion. POM cluster formation at the Moα-in and Moβ sites appears to be driven by filtering out and binding/protecting self-assembled transient species complementary to the protein template.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany. Electronic address: ulrich.ermler@biophys.mpg.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molybdenum storage protein subunit betaB270Azotobacter vinelandii DJMutation(s): 0 
Gene Names: mosBAvin_43210
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84253 
Go to UniProtKB:  P84253
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Molybdenum storage protein subunit alphaA276Azotobacter vinelandii DJMutation(s): 0 
Gene Names: mosAAvin_43200
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84308 
Go to UniProtKB:  P84308
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8M0
Query on 8M0

Download CCD File 
A, B
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
 Ligand Interaction
ATP
Query on ATP

Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
M10
Query on M10

Download CCD File 
A
(mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI)
Mo3 O13
HGNGIYFURFJYFJ-UHFFFAOYSA-N
 Ligand Interaction
MO
Query on MO

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A, B
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.585α = 90
b = 115.585β = 90
c = 234.174γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description