8P3L | pdb_00008p3l

The structure of thiocyanate dehydrogenase mutant form with Thr 169 replaced by Ala from Thioalkalivibrio paradoxus

PDB DOI: https://doi.org/10.2210/pdb8P3L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thioalkalivibrio paradoxus ARh 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-05-18 Released: 2023-05-31
Deposition Author(s): Varfolomeeva, L.A., Polyakov, K.M., Komolov, A.S., Rakitina, T.V., Dergousova, N.I., Dorovatovskii, P.V., Boyko, K.M., Tikhonova, T.V., Popov, V.O.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.254 (Depositor), 0.258 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (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

Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals

Varfolomeeva, L.A., Polyakov, K.M., Komolov, A.S., Rakitina, T.V., Dergousova, N.I., Dorovatovskii, P.V., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

(2023) Crystallogr Rep

DOI: https://doi.org/10.1134/S1063774523600990

Macromolecule Content

Total Structure Weight: 221.17 kDa
Atom Count: 15,340
Modeled Residue Count: 1,868
Deposited Residue Count: 1,976
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 [auth D], C [auth G], D [auth J]	494	Thioalkalivibrio paradoxus ARh 1	Mutation(s): 1 Gene Names: THITH_13335
UniProt
Find proteins for W0DP94 (Thioalkalivibrio paradoxus ARh 1) Explore W0DP94 Go to UniProtKB: W0DP94
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W0DP94
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain T [auth J] MOL2 format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth J] mmCIF format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain N [auth G] mmCIF format, chain O [auth G] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth J]	G [auth A] J [auth D] K [auth D] N [auth G] O [auth G] G [auth A], J [auth D], K [auth D], N [auth G], O [auth G], P [auth G], Q [auth G], T [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth J] Interactions & Density Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain T [auth J]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain R [auth J] SDF format, chain S [auth J] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain R [auth J] MOL2 format, chain S [auth J] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain L [auth G] mmCIF format, chain M [auth G] mmCIF format, chain R [auth J] mmCIF format, chain S [auth J]	E [auth A] F [auth A] H [auth D] I [auth D] L [auth G] E [auth A], F [auth A], H [auth D], I [auth D], L [auth G], M [auth G], R [auth J], S [auth J]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain L [auth G] Focus chain M [auth G] Focus chain R [auth J] Focus chain S [auth J] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain L [auth G] Focus chain M [auth G] Focus chain R [auth J] Focus chain S [auth J]