6H8H | pdb_00006h8h

Molybdenum storage protein - in a recombinant and in vivo-like form

PDB DOI: https://doi.org/10.2210/pdb6H8H/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Azotobacter vinelandii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-08-02 Released: 2018-11-14
Deposition Author(s): Ermler, U., Bruenle, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.221 (Depositor), 0.245 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Organizational Affiliation

Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, D-60438 Frankfurt/Main, Germany.

Macromolecule Content

Total Structure Weight: 64.17 kDa
Atom Count: 4,262
Modeled Residue Count: 512
Deposited Residue Count: 544
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum storage protein subunit beta	A [auth B]	269	Azotobacter vinelandii	Mutation(s): 0 Gene Names: mosB, Avin_43210
UniProt
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore P84253 Go to UniProtKB: P84253
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84253
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum storage protein subunit alpha	B [auth A]	275	Azotobacter vinelandii	Mutation(s): 0 Gene Names: mosA, Avin_43200
UniProt
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore P84308 Go to UniProtKB: P84308
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84308
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GX2 Query on GX2 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	Mo14O47 cluster H₁₇ Mo₁₄ O₄₇ CTEDOAJRLHQTLF-UHFFFAOYSA-A		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
8M0 Query on 8M0 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain C [auth B] MOL2 format, chain J [auth A] MOL2 format, chain C [auth B] mmCIF format, chain J [auth A] mmCIF format, chain C [auth B]	C [auth B], J [auth A]	bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) Mo₈ O₂₈ GSOSAILZTJNYOK-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain J [auth A] Interactions & Density Focus chain C [auth B] Focus chain J [auth A]
FUQ Query on FUQ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	Mo5 Cluster H₂₀ Mo₅ O₂₅ KKTGFJKWMBVMER-UHFFFAOYSA-A		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
M27 Query on M27 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	bis(mu2-oxo)-octaoxo-dimolybdenum (VI) Mo₂ O₁₀ OMHJAEGSJTZMPB-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
MOO Query on MOO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	MOLYBDATE ION Mo O₄ MEFBJEMVZONFCJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.221 (Depositor), 0.245 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.1	α = 90
b = 117.1	β = 90
c = 235.62	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Ermler, U.

Bruenle, S.

Revision History (Full details and data files)

Version 1.0: 2018-11-14
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