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: 64.2 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
J7T	C [auth B]	molybdate cluster Mo9 O31 OPVBNKHERKYGEI-UHFFFAOYSA-A
J8B	J [auth A]	Molybdate cluster Mo8 O26 VDJFCWAFEZEUOL-UHFFFAOYSA-A
J7Q	G [auth A]	tetrakis($l^{1}-oxidanyl)-[[2,2,2,4,4,4,4,6,6,6,8-undecakis($l^{1}-oxidanyl)-8-(oxidanylmolybdeniooxy)-6-[tris($l^{1}-oxidanyl)molybdeniooxy]-1,3,5,7-tetraoxa-2$l^{6},4$l^{6},6$l^{6},8$l^{4}-tetramolybdacyclooct-2-yl]oxy]molybdenum H Mo7 O26 JETHCXFIMFVFFB-UHFFFAOYSA-A
FUQ	F [auth B]	Mo5 Cluster H20 Mo5 O25 KKTGFJKWMBVMER-UHFFFAOYSA-A
J85	K [auth A]	[[[bis(oxidanylmolybdenio)-$l^{3}-oxidanyl]-$l^{1}-oxidanyl-oxidanylidene-molybdenio]-(oxidanylmolybdenio)-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)molybdenum H3 Mo5 O11 VWFFRZIWORKLLY-UHFFFAOYSA-F
J8E	E [auth B]	oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum H2 Mo4 O10 DPQAEXIBFYBKAN-UHFFFAOYSA-G
ATP	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
J7N	D [auth B]	2,2,4-tris(oxidanyl)-1,3-dioxa-2$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