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- PDB-6pz0: Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound... -

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Basic information

Entry
Database: PDB / ID: 6pz0
TitleCrystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and L-Tyrosine
Componentsiodotyrosine deiodinase
KeywordsOXIDOREDUCTASE / flavoprotein / dehalogenase / thermophile / halotyrosine
Function / homology
Function and homology information


L-tyrosine binding / iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / FMN binding
Similarity search - Function
: / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / TYROSINE / Iodotyrosine deiodinase
Similarity search - Component
Biological speciesThermotoga neapolitana DSM 4359 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSun, Z. / Kavran, J.M. / Rokita, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana.
Authors: Sun, Z. / Xu, B. / Spisak, S. / Kavran, J.M. / Rokita, S.E.
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iodotyrosine deiodinase
B: iodotyrosine deiodinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,27312
Polymers45,7852
Non-polymers1,48810
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-119 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.886, 81.815, 103.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein iodotyrosine deiodinase / IYD


Mass: 22892.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana DSM 4359 (bacteria)
Strain: ATCC 49049 / DSM 4359 / NS-E / Gene: CTN_0569 / Production host: Escherichia coli (E. coli) / References: UniProt: B9K712, iodotyrosine deiodinase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium citrate, pH 4.5, 3 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.799→35.67 Å / Num. obs: 34678 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.845.90.2241158419650.9730.0990.2455.197.7
8.99-35.6760.04820223360.9970.0210.05225.398.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5K08

5k08


Resolution: 1.8→35.669 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 18.58
RfactorNum. reflection% reflection
Rfree0.1964 1761 5.09 %
Rwork0.1494 --
obs0.1519 34620 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.14 Å2 / Biso mean: 23.8478 Å2 / Biso min: 6.85 Å2
Refinement stepCycle: final / Resolution: 1.8→35.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 148 385 3622
Biso mean--15.34 31.15 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113303
X-RAY DIFFRACTIONf_angle_d1.2334486
X-RAY DIFFRACTIONf_chiral_restr0.045468
X-RAY DIFFRACTIONf_plane_restr0.007562
X-RAY DIFFRACTIONf_dihedral_angle_d13.3331308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.84740.22381270.1618244298
1.8474-1.90180.20321430.14972483100
1.9018-1.96320.24951460.15762482100
1.9632-2.03330.23341340.15422478100
2.0333-2.11470.23691030.14792538100
2.1147-2.2110.18891260.14242519100
2.211-2.32750.21711400.14252499100
2.3275-2.47330.19971340.14852513100
2.4733-2.66420.2251490.15582523100
2.6642-2.93220.1961380.16732520100
2.9322-3.35620.19931400.15652553100
3.3562-4.22740.15511300.13142600100
4.2274-35.6690.17611510.15042709100

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