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- PDB-5yak: The crystal structure of human IYD Thr239 mutant with ligand 3-Fl... -

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Basic information

Entry
Database: PDB / ID: 5yak
TitleThe crystal structure of human IYD Thr239 mutant with ligand 3-Fluorotyrosine (F-Tyr)
ComponentsIodotyrosine deiodinase 1
KeywordsOXIDOREDUCTASE / hIYD / FMN / MFT / T239A mutant
Function / homology
Function and homology information


iodotyrosine deiodinase / iodotyrosine deiodinase activity / Thyroxine biosynthesis / thyroid hormone metabolic process / tyrosine metabolic process / cytoplasmic vesicle membrane / FMN binding / oxidoreductase activity / nucleoplasm / plasma membrane
Similarity search - Function
: / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 3-FLUOROTYROSINE / Iodotyrosine deiodinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHu, J.M. / Rokita, S.E. / Schlessman, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthDK084186 United States
Citation
Journal: Protein Sci. / Year: 2019
Title: Redox control of iodotyrosine deiodinase
Authors: Hu, J. / Su, Q. / Schlessman, J.L. / Rokita, S.E.
#1: Journal: To Be Published
Title: The role of Thr239 on the catalysis of hIYD
Authors: Hu, J.M. / Rokita, S.E.
History
DepositionSep 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 1
B: Iodotyrosine deiodinase 1
C: Iodotyrosine deiodinase 1
D: Iodotyrosine deiodinase 1
E: Iodotyrosine deiodinase 1
F: Iodotyrosine deiodinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,16118
Polymers183,2286
Non-polymers3,93312
Water5,350297
1
A: Iodotyrosine deiodinase 1
F: Iodotyrosine deiodinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3876
Polymers61,0762
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-73 kcal/mol
Surface area18460 Å2
MethodPISA
2
B: Iodotyrosine deiodinase 1
C: Iodotyrosine deiodinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3876
Polymers61,0762
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-74 kcal/mol
Surface area18280 Å2
MethodPISA
3
D: Iodotyrosine deiodinase 1
E: Iodotyrosine deiodinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3876
Polymers61,0762
Non-polymers1,3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-73 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.079, 105.079, 300.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Iodotyrosine deiodinase 1 / IYD-1 / Iodotyrosine dehalogenase 1


Mass: 30537.951 Da / Num. of mol.: 6 / Fragment: UNP residues 32-289 / Mutation: T239A
Source method: isolated from a genetically manipulated source
Details: FMN(flavin mononucleotide) YOF(3-monofluorotyrosine)
Source: (gene. exp.) Homo sapiens (human) / Gene: IYD, C6orf71, DEHAL1 / Plasmid: pET28-SUMO / Details (production host): sumo fusion N-terminal / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q6PHW0, iodotyrosine deiodinase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-YOF / 3-FLUOROTYROSINE


Type: L-peptide linking / Mass: 199.179 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H10FNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.17 M sodium acetate, 85 mM Tris-HCl (pH 8.5), 22.5 % w/v polyethylene glycol 4,000 and 15 % glycerol.
PH range: 7.4-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.52 Å / Num. obs: 82734 / % possible obs: 100 % / Redundancy: 8 % / Net I/σ(I): 41.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8 % / Rmerge(I) obs: 0.093 / Rsym value: 0.084 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TTC

4ttc


Resolution: 2.3→46.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.199 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22622 4144 5 %RANDOM
Rwork0.18303 ---
obs0.18526 78650 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.406 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.3→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10536 0 270 297 11103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911058
X-RAY DIFFRACTIONr_bond_other_d00.0210958
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.99815005
X-RAY DIFFRACTIONr_angle_other_deg3.433325229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45651292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98923.333459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.129152006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7141578
X-RAY DIFFRACTIONr_chiral_restr0.0920.21685
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111900
X-RAY DIFFRACTIONr_gen_planes_other0.0140.022402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9254.515219
X-RAY DIFFRACTIONr_mcbond_other3.9254.515219
X-RAY DIFFRACTIONr_mcangle_it5.2286.7416494
X-RAY DIFFRACTIONr_mcangle_other5.2286.7416495
X-RAY DIFFRACTIONr_scbond_it4.8545.0245839
X-RAY DIFFRACTIONr_scbond_other4.8545.0235840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1297.2958512
X-RAY DIFFRACTIONr_long_range_B_refined8.46536.44913142
X-RAY DIFFRACTIONr_long_range_B_other8.47936.43413063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 293 -
Rwork0.215 5790 -
obs--99.79 %

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