6H8B

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.234 (Depositor), 0.240 (DCC)
R-Value Observed:
0.234 (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 of 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: 64.2 kDa
Atom Count: 4,238
Modelled Residue Count: 513
Deposited Residue Count: 544
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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
UniProt
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore P84253 Go to UniProtKB: P84253
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84253
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 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
UniProt
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore P84308 Go to UniProtKB: P84308
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84308
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J7T Query on J7T Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	molybdate cluster Mo₉ O₃₁ OPVBNKHERKYGEI-UHFFFAOYSA-A		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
J8B Query on J8B Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	Molybdate cluster Mo₈ O₂₆ VDJFCWAFEZEUOL-UHFFFAOYSA-A		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
J7Q Query on J7Q Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	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$l^{4}-tetramolybdacyclooct-2-yl]oxy]molybdenum H Mo₇ O₂₆ JETHCXFIMFVFFB-UHFFFAOYSA-A		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
FUQ Query on FUQ Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	Mo5 Cluster H₂₀ Mo₅ O₂₅ KKTGFJKWMBVMER-UHFFFAOYSA-A		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
J85 Query on J85 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	[[[bis(oxidanylmolybdenio)-$l^{3}-oxidanyl]-$l^{1}-oxidanyl-oxidanylidene-molybdenio]-(oxidanylmolybdenio)-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)molybdenum H₃ Mo₅ O₁₁ VWFFRZIWORKLLY-UHFFFAOYSA-F		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
J8E Query on J8E Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum H₂ Mo₄ O₁₀ DPQAEXIBFYBKAN-UHFFFAOYSA-G		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
J7N Query on J7N Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	2,2,4-tris(oxidanyl)-1,3-dioxa-2$l^{4},4$l^{3}-dimolybdacyclobutane H₃ Mo₂ O₅ AUVZZTGQIKYYRK-UHFFFAOYSA-K		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MOO Query on MOO 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]	MOLYBDATE ION Mo O₄ MEFBJEMVZONFCJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
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: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.234 (Depositor), 0.240 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-02-20

Deposition Author(s):

Ermler, U.

Poppe, J.

Revision History (Full details and data files)

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