6TYK | pdb_00006tyk

Crystal structure of iodotyrosine deiodinase (IYD) in the semiquinone form bound to FMN and 3-iodo-L-tyrosine

PDB DOI: https://doi.org/10.2210/pdb6TYK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga neapolitana DSM 4359
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-08-09 Released: 2021-04-07
Deposition Author(s): Sun, Z., Kavran, J.M., Rokita, S.E.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.194 (Depositor), 0.196 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Structure of Tn IYD bound in the semiquinone form bound to FMN and 3-iodo-L-tyrosine

Sun, Z., Kavran, J.M., Rokita, S.E.

To be published.

Macromolecule Content

Total Structure Weight: 47.87 kDa
Atom Count: 3,566
Modeled Residue Count: 369
Deposited Residue Count: 384
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
iodotyrosine deiodinase	A, B	192	Thermotoga neapolitana DSM 4359	Mutation(s): 0 Gene Names: CTN_0569 EC: 1.21.1.1
UniProt
Find proteins for B9K712 (Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NBRC 107923 / NS-E)) Explore B9K712 Go to UniProtKB: B9K712
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9K712
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
IYR (Subject of Investigation/LOI) Query on IYR Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B], N [auth B]	3-IODO-TYROSINE C₉ H₁₀ I N O₃ UQTZMGFTRHFAAM-ZETCQYMHSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.194 (Depositor), 0.196 (DCC)
R-Value Work: 0.158 (Depositor), 0.159 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.035	α = 90
b = 81.176	β = 90
c = 104.146	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.