6H8B | pdb_00006h8b

Molybdenum storage protein prepared under in vivo-like conditions and incubated with ATP and molybdate at 303 K

• PDB DOI: https://doi.org/10.2210/pdb6H8B/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2018-08-02 Released: 2019-02-20 
• Deposition Author(s): Ermler, U., Poppe, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

The molybdenum storage protein - A bionanolab for creating experimentally alterable polyoxomolybdate clusters.

Brunle, S., Poppe, J., Hail, R., Demmer, U., Ermler, U.

(2018) J Inorg Biochem 189: 172-179

• PubMed: 30278367 
• DOI: https://doi.org/10.1016/j.jinorgbio.2018.09.011
• Primary Citation Related Structures: 
  6GWB, 6H6W, 6H73, 6H74, 6H8B, 6H8H

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Organizational Affiliation: 
• Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, D-60438 Frankfurt/Main, Germany.
Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, D-60438 Frankfurt/Main, Germany; Biochemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany.
Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, D-60438 Frankfurt/Main, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.71 kDa 
• Atom Count: 4,238 
• Modeled Residue Count: 513 
• Deposited Residue Count: 544 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum storage protein subunit beta	A [auth B]	269	Azotobacter vinelandii	Mutation(s): 0
UniProt
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore P84253  Go to UniProtKB:  P84253

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum storage protein subunit alpha	B [auth A]	275	Azotobacter vinelandii	Mutation(s): 0
UniProt
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore P84308  Go to UniProtKB:  P84308

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JID	K [auth A]	polyoxomolybdate cluster Mo11 H3 Mo11 O29 FJRLUCFNPRJGEM-UHFFFAOYSA-A
J7T	C [auth B]	molybdate cluster Mo9 O31 OPVBNKHERKYGEI-UHFFFAOYSA-A
8M0	J [auth A]	bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) Mo8 O28 GSOSAILZTJNYOK-UHFFFAOYSA-N
JLF	E [auth B]	polyoxomolybdate cluster Mo8 Mo8 O26 VDJFCWAFEZEUOL-UHFFFAOYSA-A
J7Q	G [auth A]	1,3,3,3,5,7,7,9,9,9,11,11,11,11,13,13,13-heptadecakis($l^{1}-oxidanyl)-2$l^{4},4,6,8,10,12,14,15,16-nonaoxa-1$l^{4},3$l^{6},5$l^{4},7$l^{5},9$l^{6},11$l^{6},13$l^{6}-heptamolybdapentacyclo[7.5.1.1^{3,13}.0^{2,5}.0^{2,7}]hexadecane Mo7 O26 QGNBBJYGPLOTFJ-UHFFFAOYSA-A
FUQ	F [auth B]	Mo5 Cluster Mo5 O25 KKTGFJKWMBVMER-UHFFFAOYSA-A
ATP	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
J7N	D [auth B]	2,2,4-tris(oxidanyl)-1,3-dioxa-2$l^{4},4$l^{3}-dimolybdacyclobutane H3 Mo2 O5 AUVZZTGQIKYYRK-UHFFFAOYSA-K
MOO	L [auth A]	MOLYBDATE ION Mo O4 MEFBJEMVZONFCJ-UHFFFAOYSA-N
MG	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.72	α = 90
b = 116.72	β = 90
c = 235.42	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Ermler, U., Poppe, J.

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 2.0: 2026-08-26
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary