4NDR

Crystal structure Molybdenum Storage Protein with fully Mo-loaded cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 

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
  • Primary Citation of Related Structures:  

  • 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

    Biochemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany.,Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany. Electronic address: ulrich.ermler@biophys.mpg.de.,Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany.,Biochemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany. Electronic address: klaus.schneider1@uni-bielefeld.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molybdenum storage protein subunit beta
B
270Azotobacter vinelandii (strain DJ / ATCC BAA-1303)Mutation(s): 0 
Gene Names: mosB
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Go to UniProtKB:  P84253
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Molybdenum storage protein subunit alpha
A
276Azotobacter vinelandii (strain DJ / ATCC BAA-1303)Mutation(s): 0 
Gene Names: mosA
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Go to UniProtKB:  P84308
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MO
Query on MO

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Download CCD File 
A, B
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
8M0
Query on 8M0

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Download CCD File 
A, B
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Octamolybdate [Mo(VI)8O28]8-
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
 Ligand Interaction
M10
Query on M10

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Download CCD File 
A
(mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI)
Trimolybdate [Mo(VI)3O13]8-
Mo3 O13
HGNGIYFURFJYFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 114.270α = 90.00
b = 114.270β = 90.00
c = 234.140γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
REFMACphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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