8Z75 | pdb_00008z75

The structure of non-activated thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH)

PDB DOI: https://doi.org/10.2210/pdb8Z75/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pelomicrobium methylotrophicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-19 Released: 2024-05-08
Deposition Author(s): Varfolomeeva, L.A., Solovieva, A.Y., Shipkov, N.S., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.196 (Depositor), 0.202 (DCC)
R-Value Work:
0.167 (Depositor), 0.173 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Effect of Copper Ions on the Crystal Packing and Conformation of Thiocyanate Dehydrogenase in the Crystal Structure

Varfolomeeva, L.A., Solovieva, A.Y., Shipkov, N.S., Dergousova, N.I., Minyaev, M.E., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

(2025) Crystallogr Rep 70: 8-15

DOI: https://doi.org/10.1134/S1063774524602478

Macromolecule Content

Total Structure Weight: 163.3 kDa
Atom Count: 12,307
Modeled Residue Count: 1,390
Deposited Residue Count: 1,467
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine translocation signal domain-containing protein	A, B, C	489	Pelomicrobium methylotrophicum	Mutation(s): 0 Gene Names: FR698_09980
UniProt
Find proteins for A0A5C7ETD9 (Pelomicrobium methylotrophicum) Explore A0A5C7ETD9 Go to UniProtKB: A0A5C7ETD9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5C7ETD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth C] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B]	G [auth A], M [auth B], T [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain T [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] H [auth B] I [auth B] J [auth B] D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], Q [auth C], R [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth C] Focus chain R [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain S [auth C] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain S [auth C]