8P3M

The structure of thiocyanate dehydrogenase mutant form with Lys 281 replaced by Ala from Thioalkalivibrio paradoxus

PDB DOI: https://doi.org/10.2210/pdb8P3M/pdb

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

Deposited: 2023-05-18 Released: 2023-06-07
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: 2.07 Å
R-Value Free: 0.234
R-Value Work: 0.179
R-Value Observed: 0.182

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: 882.95 kDa
Atom Count: 60,462
Modelled Residue Count: 7,472
Deposited Residue Count: 7,904
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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] E [auth M] A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P], G [auth S], H [auth V], I [auth Y], J [auth 2], K [auth 5], L [auth 8], M [auth x], N [auth e], O [auth h], P [auth k]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W0DP94
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth J] SDF format, chain DB [auth 8] SDF format, chain GB [auth x] SDF format, chain IA [auth P] SDF format, chain NA [auth S] SDF format, chain U [auth A] SDF format, chain UA [auth Y] SDF format, chain V [auth D] SDF format, chain XA [auth 2] SDF format, chain Z [auth G] SDF format, chain AB [auth 5] SDF format, chain FA [auth M] SDF format, chain JA [auth P] SDF format, chain LB [auth h] SDF format, chain OB [auth k] SDF format, chain Q [auth A] SDF format, chain QA [auth V] MOL2 format, chain CA [auth J] MOL2 format, chain DB [auth 8] MOL2 format, chain GB [auth x] MOL2 format, chain IA [auth P] MOL2 format, chain NA [auth S] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth Y] MOL2 format, chain V [auth D] MOL2 format, chain XA [auth 2] MOL2 format, chain Z [auth G] MOL2 format, chain AB [auth 5] MOL2 format, chain FA [auth M] MOL2 format, chain JA [auth P] MOL2 format, chain LB [auth h] MOL2 format, chain OB [auth k] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth V] mmCIF format, chain CA [auth J] mmCIF format, chain DB [auth 8] mmCIF format, chain GB [auth x] mmCIF format, chain IA [auth P] mmCIF format, chain NA [auth S] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth Y] mmCIF format, chain V [auth D] mmCIF format, chain XA [auth 2] mmCIF format, chain Z [auth G] mmCIF format, chain AB [auth 5] mmCIF format, chain FA [auth M] mmCIF format, chain JA [auth P] mmCIF format, chain LB [auth h] mmCIF format, chain OB [auth k] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth V]	AB [auth 5] CA [auth J] DB [auth 8] FA [auth M] GB [auth x] AB [auth 5], CA [auth J], DB [auth 8], FA [auth M], GB [auth x], IA [auth P], JA [auth P], LB [auth h], NA [auth S], OB [auth k], Q [auth A], QA [auth V], U [auth A], UA [auth Y], V [auth D], XA [auth 2], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth 5] Focus chain CA [auth J] Focus chain DB [auth 8] Focus chain FA [auth M] Focus chain GB [auth x] Focus chain IA [auth P] Focus chain JA [auth P] Focus chain LB [auth h] Focus chain NA [auth S] Focus chain OB [auth k] Focus chain Q [auth A] Focus chain QA [auth V] Focus chain U [auth A] Focus chain UA [auth Y] Focus chain V [auth D] Focus chain XA [auth 2] Focus chain Z [auth G] Interactions & Density Focus chain AB [auth 5] Focus chain CA [auth J] Focus chain DB [auth 8] Focus chain FA [auth M] Focus chain GB [auth x] Focus chain IA [auth P] Focus chain JA [auth P] Focus chain LB [auth h] Focus chain NA [auth S] Focus chain OB [auth k] Focus chain Q [auth A] Focus chain QA [auth V] Focus chain U [auth A] Focus chain UA [auth Y] Focus chain V [auth D] Focus chain XA [auth 2] Focus chain Z [auth G]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain BB [auth 5] SDF format, chain CB [auth 5] SDF format, chain EB [auth 8] SDF format, chain FB [auth 8] SDF format, chain GA [auth M] SDF format, chain IB [auth x] SDF format, chain JB [auth e] SDF format, chain KB [auth e] SDF format, chain LA [auth P] SDF format, chain NB [auth h] SDF format, chain PA [auth S] SDF format, chain PB [auth k] SDF format, chain QB [auth k] SDF format, chain RA [auth V] SDF format, chain SA [auth V] SDF format, chain T [auth A] SDF format, chain VA [auth Y] SDF format, chain WA [auth Y] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain YA [auth 2] SDF format, chain ZA [auth 2] SDF format, chain DA [auth J] SDF format, chain EA [auth J] SDF format, chain HA [auth M] SDF format, chain HB [auth x] SDF format, chain KA [auth P] SDF format, chain MB [auth h] SDF format, chain OA [auth S] SDF format, chain S [auth A] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain BB [auth 5] MOL2 format, chain CB [auth 5] MOL2 format, chain EB [auth 8] MOL2 format, chain FB [auth 8] MOL2 format, chain GA [auth M] MOL2 format, chain IB [auth x] MOL2 format, chain JB [auth e] MOL2 format, chain KB [auth e] MOL2 format, chain LA [auth P] MOL2 format, chain NB [auth h] MOL2 format, chain PA [auth S] MOL2 format, chain PB [auth k] MOL2 format, chain QB [auth k] MOL2 format, chain RA [auth V] MOL2 format, chain SA [auth V] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth Y] MOL2 format, chain WA [auth Y] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth 2] MOL2 format, chain ZA [auth 2] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth J] MOL2 format, chain HA [auth M] MOL2 format, chain HB [auth x] MOL2 format, chain KA [auth P] MOL2 format, chain MB [auth h] MOL2 format, chain OA [auth S] MOL2 format, chain S [auth A] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain BB [auth 5] mmCIF format, chain CB [auth 5] mmCIF format, chain EB [auth 8] mmCIF format, chain FB [auth 8] mmCIF format, chain GA [auth M] mmCIF format, chain IB [auth x] mmCIF format, chain JB [auth e] mmCIF format, chain KB [auth e] mmCIF format, chain LA [auth P] mmCIF format, chain NB [auth h] mmCIF format, chain PA [auth S] mmCIF format, chain PB [auth k] mmCIF format, chain QB [auth k] mmCIF format, chain RA [auth V] mmCIF format, chain SA [auth V] mmCIF format, chain T [auth A] mmCIF format, chain VA [auth Y] mmCIF format, chain WA [auth Y] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth 2] mmCIF format, chain ZA [auth 2] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth J] mmCIF format, chain HA [auth M] mmCIF format, chain HB [auth x] mmCIF format, chain KA [auth P] mmCIF format, chain MB [auth h] mmCIF format, chain OA [auth S] mmCIF format, chain S [auth A]	AA [auth G] BA [auth G] BB [auth 5] CB [auth 5] DA [auth J] AA [auth G], BA [auth G], BB [auth 5], CB [auth 5], DA [auth J], EA [auth J], EB [auth 8], FB [auth 8], GA [auth M], HA [auth M], HB [auth x], IB [auth x], JB [auth e], KA [auth P], KB [auth e], LA [auth P], MB [auth h], NB [auth h], OA [auth S], PA [auth S], PB [auth k], QB [auth k], RA [auth V], S [auth A], SA [auth V], T [auth A], VA [auth Y], WA [auth Y], X [auth D], Y [auth D], YA [auth 2], ZA [auth 2]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain BB [auth 5] Focus chain CB [auth 5] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain EB [auth 8] Focus chain FB [auth 8] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain HB [auth x] Focus chain IB [auth x] Focus chain JB [auth e] Focus chain KA [auth P] Focus chain KB [auth e] Focus chain LA [auth P] Focus chain MB [auth h] Focus chain NB [auth h] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain PB [auth k] Focus chain QB [auth k] Focus chain RA [auth V] Focus chain S [auth A] Focus chain SA [auth V] Focus chain T [auth A] Focus chain VA [auth Y] Focus chain WA [auth Y] Focus chain X [auth D] Focus chain Y [auth D] Focus chain YA [auth 2] Focus chain ZA [auth 2] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain BB [auth 5] Focus chain CB [auth 5] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain EB [auth 8] Focus chain FB [auth 8] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain HB [auth x] Focus chain IB [auth x] Focus chain JB [auth e] Focus chain KA [auth P] Focus chain KB [auth e] Focus chain LA [auth P] Focus chain MB [auth h] Focus chain NB [auth h] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain PB [auth k] Focus chain QB [auth k] Focus chain RA [auth V] Focus chain S [auth A] Focus chain SA [auth V] Focus chain T [auth A] Focus chain VA [auth Y] Focus chain WA [auth Y] Focus chain X [auth D] Focus chain Y [auth D] Focus chain YA [auth 2] Focus chain ZA [auth 2]
BO3 Query on BO3 Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth A]	R [auth A], W [auth D]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain W [auth D] Interactions & Density Focus chain R [auth A] Focus chain W [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain TA [auth V] SDF format, chain MA [auth P] MOL2 format, chain TA [auth V] MOL2 format, chain MA [auth P] mmCIF format, chain TA [auth V] mmCIF format, chain MA [auth P]	MA [auth P], TA [auth V]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain MA [auth P] Focus chain TA [auth V] Interactions & Density Focus chain MA [auth P] Focus chain TA [auth V]