5OEX | pdb_00005oex

Complex with iodine ion for thiocyanate dehydrogenase from Thioalkalivibrio paradoxus

PDB DOI: https://doi.org/10.2210/pdb5OEX/pdb
Entry: 5OEX supersedes: 5F30

Classification: OXIDOREDUCTASE
Organism(s): Thioalkalivibrio paradoxus ARh 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-07-10 Released: 2018-08-01
Deposition Author(s): Polyakov, K.M., Tsallagov, S.I., Tikhonova, T.V., Popov, V.O.
Funding Organization(s): Russian Science Fondation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery and characterization of a novel copper containing enzyme - THIOCYANATE DEHYDROGENASE.

Tikhonova, T.V., Sorokin, D.I., Tsallagov, S.I., Polyakov, K.M., Trofimov, A.A., Shabalin, I.G., Khrenova, M.G., Muyser, G., Rakitina, T.V., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 209.26 kDa
Atom Count: 15,588
Modeled Residue Count: 1,868
Deposited Residue Count: 1,868
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THIOCYANATE DEHYDROGENASE	A, B, C, D	467	Thioalkalivibrio paradoxus ARh 1	Mutation(s): 0 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4G Query on P4G Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D]	DA [auth D] EA [auth D] FA [auth D] J [auth A] K [auth A] DA [auth D], EA [auth D], FA [auth D], J [auth A], K [auth A], L [auth A], X [auth C], Y [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth C] Focus chain Y [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] E [auth A] F [auth A] AA [auth D], BA [auth D], CA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], T [auth C], U [auth C], V [auth C], W [auth C], Z [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B]	P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.198 (Depositor), 0.199 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.82	α = 90
b = 159.45	β = 97.77
c = 91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-01

Deposition Author(s):

This entry supersedes: 5F30

Funding Organization	Location	Grant Number
Russian Science Fondation	Russian Federation	15-14-00063

Revision History (Full details and data files)

Version 1.0: 2018-08-01
Type: Initial release
Version 1.1: 2018-10-03
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description