7ZCC | pdb_00007zcc

yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)

PDB DOI: https://doi.org/10.2210/pdb7ZCC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-27 Released: 2023-04-05
Deposition Author(s): Chowdhury, R., Schofield, C.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.165 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

yxBC from Bacillus subtilis in complex with Mn and N-oxalylglycine (NOG)

Chowdhury, R., Schofield, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 158.44 kDa
Atom Count: 11,295
Modeled Residue Count: 1,301
Deposited Residue Count: 1,364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YxbC	A, B, C, D	341	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: yxbC, yxaQ, BSU39880, VE7D
UniProt
Find proteins for P46327 (Bacillus subtilis (strain 168)) Explore P46327 Go to UniProtKB: P46327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46327
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OGA (Subject of Investigation/LOI) Query on OGA Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain U [auth C] SDF format, chain O [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B]	CA [auth D], F [auth A], O [auth B], U [auth C]	N-OXALYLGLYCINE C₄ H₅ N O₅ BIMZLRFONYSTPT-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain KA [auth D] SDF format, chain IA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain IA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain JA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain IA [auth D]	AA [auth C] IA [auth D] JA [auth D] KA [auth D] L [auth A] AA [auth C], IA [auth D], JA [auth D], KA [auth D], L [auth A], M [auth A], R [auth B], S [auth B], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth D] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain FA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D]	DA [auth D] EA [auth D] FA [auth D] G [auth A] GA [auth D] DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], V [auth C], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain E [auth A] SDF format, chain BA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth D]	BA [auth D], E [auth A], N [auth B], T [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain T [auth C]