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- PDB-6tyk: Crystal structure of iodotyrosine deiodinase (IYD) in the semiqui... -

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Basic information

Entry
Database: PDB / ID: 6tyk
TitleCrystal structure of iodotyrosine deiodinase (IYD) in the semiquinone form bound to FMN and 3-iodo-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
: / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 3-IODO-TYROSINE / Iodotyrosine deiodinase
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 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: To Be Published
Title: Structure of Tn IYD bound in the semiquinone form bound to FMN and 3-iodo-L-tyrosine
Authors: Sun, Z. / Kavran, J.M. / Rokita, S.E.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,86714
Polymers45,7852
Non-polymers2,08212
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-134 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.035, 81.176, 104.146
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 (strain ATCC 49049 / DSM 4359 / NS-E) (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-IYR / 3-IODO-TYROSINE


Type: L-peptide linking / Mass: 307.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H10INO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 38.08 %
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: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.35→38.02 Å / Num. obs: 80875 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 14.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.043 / Rrim(I) all: 0.102 / Net I/σ(I): 8.2 / Num. measured all: 437630 / Scaling rejects: 1422
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
1.35-1.374.91.4871938039260.4590.7411.6681.699
7.39-38.025.20.0830525860.9920.0370.08816.299.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.35→37.818 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 4063 5.03 %
Rwork0.1577 76682 -
obs0.1595 80745 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.1 Å2 / Biso mean: 20.0256 Å2 / Biso min: 7.88 Å2
Refinement stepCycle: final / Resolution: 1.35→37.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 176 342 3591
Biso mean--18.07 34.24 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053312
X-RAY DIFFRACTIONf_angle_d1.0064506
X-RAY DIFFRACTIONf_chiral_restr0.065471
X-RAY DIFFRACTIONf_plane_restr0.005564
X-RAY DIFFRACTIONf_dihedral_angle_d12.3291294
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.36580.27481210.242256298
1.3658-1.38240.27191390.22332630100
1.3824-1.39990.27431400.21622598100
1.3999-1.41840.25721380.21032618100
1.4184-1.43780.26281570.20372594100
1.4378-1.45830.28811170.20612642100
1.4583-1.48010.2681520.19792615100
1.4801-1.50320.26151360.18712616100
1.5032-1.52790.2461330.18012634100
1.5279-1.55420.20931420.17062604100
1.5542-1.58250.2191370.1612601100
1.5825-1.61290.20051410.15332623100
1.6129-1.64580.18271280.15062646100
1.6458-1.68160.23351260.14852621100
1.6816-1.72080.19491400.14312647100
1.7208-1.76380.19661480.14452626100
1.7638-1.81150.17781350.14272632100
1.8115-1.86480.20761460.14622636100
1.8648-1.9250.20111520.14472612100
1.925-1.99380.1861560.13932630100
1.9938-2.07360.16741180.13882697100
2.0736-2.16790.19541270.13892673100
2.1679-2.28220.16961470.13612639100
2.2822-2.42520.19361440.15282664100
2.4252-2.61240.2241560.1609264399
2.6124-2.87520.17621460.17142701100
2.8752-3.29110.18791410.16452692100
3.2911-4.14560.15581410.14022727100
4.1456-37.8180.18621590.16772859100

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