8RQZ | pdb_00008rqz

Crystal structure of Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1 from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb8RQZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Mutation(s): No

Deposited: 2024-01-22 Released: 2025-08-06
Deposition Author(s): Cherrier, M.V., Arnoux, P., Martin, L., Nicolet, Y., Schoehn, G., Legrand, P., Broc, M., Seduk, F., Brasseur, G., Arias-Cartin, R., Magalon, A., Walburger, A., Uzel, A., Guigliarelli, B., Grimaldi, S., Pierrel, F., Mate, M.
Funding Organization(s): Agence Nationale de la Recherche (ANR), French Infrastructure for Integrated Structural Biology (FRISBI), Grenoble Alliance for Integrated Structural Cell Biology (GRAL), Centre National de la Recherche Scientifique (CNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.231 (Depositor), 0.223 (DCC)
R-Value Work:
0.196 (Depositor), 0.191 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Conserved Helical Membrane Plug-in for Quinone reductases

Cherrier, M.V., Arnoux, P., Martin, L., Nicolet, Y., Schoehn, G., Legrand, P., Broc, M., Seduk, F., Brasseur, G., Arias-Cartin, R., Magalon, A., Walburger, A., Uzel, A., Guigliarelli, B., Grimaldi, S., Pierrel, F., Mate, M.

To be published.

Macromolecule Content

Total Structure Weight: 274.67 kDa
Atom Count: 18,937
Modeled Residue Count: 2,244
Deposited Residue Count: 2,342
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YjgD	A, B	186	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0
UniProt
Find proteins for O34681 (Bacillus subtilis (strain 168)) Explore O34681 Go to UniProtKB: O34681
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34681
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable oxidoreductase YjgC	C, D	985	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 EC: 1
UniProt
Find proteins for O34720 (Bacillus subtilis (strain 168)) Explore O34720 Go to UniProtKB: O34720
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain QA [auth D] SDF format, chain R [auth C] SDF format, chain RA [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth D]	Q [auth C], QA [auth D], R [auth C], RA [auth D]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain Q [auth C] Focus chain QA [auth D] Focus chain R [auth C] Focus chain RA [auth D] Interactions & Density Focus chain Q [auth C] Focus chain QA [auth D] Focus chain R [auth C] Focus chain RA [auth D]
LHG Query on LHG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain X [auth C] MOL2 format, chain K [auth B] MOL2 format, chain X [auth C] mmCIF format, chain K [auth B] mmCIF format, chain X [auth C]	K [auth B], X [auth C]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain K [auth B] Focus chain X [auth C] Interactions & Density Focus chain K [auth B] Focus chain X [auth C]
MQ7 (Subject of Investigation/LOI) Query on MQ7 Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain TA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth D] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth D]	T [auth C], TA [auth D]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain T [auth C] Focus chain TA [auth D] Interactions & Density Focus chain T [auth C] Focus chain TA [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain MA [auth D] SDF format, chain N [auth C] SDF format, chain NA [auth D] SDF format, chain O [auth C] SDF format, chain OA [auth D] SDF format, chain P [auth C] SDF format, chain PA [auth D] MOL2 format, chain M [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth C] MOL2 format, chain PA [auth D] mmCIF format, chain M [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth C] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth C] mmCIF format, chain PA [auth D]	M [auth C] MA [auth D] N [auth C] NA [auth D] O [auth C] M [auth C], MA [auth D], N [auth C], NA [auth D], O [auth C], OA [auth D], P [auth C], PA [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain MA [auth D] Focus chain N [auth C] Focus chain NA [auth D] Focus chain O [auth C] Focus chain OA [auth D] Focus chain P [auth C] Focus chain PA [auth D] Interactions & Density Focus chain M [auth C] Focus chain MA [auth D] Focus chain N [auth C] Focus chain NA [auth D] Focus chain O [auth C] Focus chain OA [auth D] Focus chain P [auth C] Focus chain PA [auth D]
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	BA [auth C], E [auth A], F [auth A], I [auth B], J [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
FES (Subject of Investigation/LOI) Query on FES Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain LA [auth D] MOL2 format, chain L [auth C] MOL2 format, chain LA [auth D] mmCIF format, chain L [auth C] mmCIF format, chain LA [auth D]	L [auth C], LA [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain LA [auth D] Interactions & Density Focus chain L [auth C] Focus chain LA [auth D]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain IA [auth D] SDF format, chain V [auth C] SDF format, chain VA [auth D] SDF format, chain W [auth C] SDF format, chain Z [auth C] SDF format, chain ZA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth D]	EA [auth C] FA [auth C] GA [auth C] IA [auth D] V [auth C] EA [auth C], FA [auth C], GA [auth C], IA [auth D], V [auth C], VA [auth D], W [auth C], Z [auth C], ZA [auth D]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain V [auth C] Focus chain VA [auth D] Focus chain W [auth C] Focus chain Z [auth C] Focus chain ZA [auth D] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain V [auth C] Focus chain VA [auth D] Focus chain W [auth C] Focus chain Z [auth C] Focus chain ZA [auth D]
4MO (Subject of Investigation/LOI) Query on 4MO Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain SA [auth D] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth D] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth D]	S [auth C], SA [auth D]	MOLYBDENUM(IV) ION Mo ZIKKVZAYJJZBGE-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Focus chain SA [auth D] Interactions & Density Focus chain S [auth C] Focus chain SA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain JA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain YA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D]	CA [auth C] DA [auth C] G [auth A] H [auth B] JA [auth D] CA [auth C], DA [auth C], G [auth A], H [auth B], JA [auth D], WA [auth D], XA [auth D], YA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain H [auth B] Focus chain JA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain H [auth B] Focus chain JA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] SDF format, chain KA [auth D] SDF format, chain Y [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain Y [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain Y [auth C]	AA [auth C], HA [auth D], KA [auth D], Y [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain KA [auth D] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain KA [auth D] Focus chain Y [auth C]
H2S (Subject of Investigation/LOI) Query on H2S Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain UA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth D]	U [auth C], UA [auth D]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Focus chain UA [auth D] Interactions & Density Focus chain U [auth C] Focus chain UA [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth D] MOL2 format, chain AB [auth D] mmCIF format, chain AB [auth D]	AB [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Interactions & Density Focus chain AB [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.231 (Depositor), 0.223 (DCC)
R-Value Work: 0.196 (Depositor), 0.191 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.833	α = 90
b = 210.5	β = 90
c = 494.213	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-15-IDEX-02
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)	France	ANR-17-EURE-0003
Agence Nationale de la Recherche (ANR)	France	ANR-22-CE44-0035-01
Centre National de la Recherche Scientifique (CNRS)	France	MICROBIOCO2
Agence Nationale de la Recherche (ANR)	France	ANR 16-CE29-0010-01