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- PDB-4tr3: Mouse iodothyronine deiodinase 3 catalytic core, SeMet-labeled ac... -

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Basic information

Entry
Database: PDB / ID: 4tr3
TitleMouse iodothyronine deiodinase 3 catalytic core, SeMet-labeled active site mutant SeCys->Cys
ComponentsType III iodothyronine deiodinase
KeywordsOXIDOREDUCTASE / deiodinase / thyronine hormones / thioredoxin fold
Function / homology
Function and homology information


thyroxine 5-deiodinase / thyroxine 5-deiodinase activity / thyroxine 5'-deiodinase activity / thyroid hormone catabolic process / Regulation of thyroid hormone activity / retinal cone cell apoptotic process / brown fat cell proliferation / hormone biosynthetic process / retinal cone cell development / positive regulation of multicellular organism growth ...thyroxine 5-deiodinase / thyroxine 5-deiodinase activity / thyroxine 5'-deiodinase activity / thyroid hormone catabolic process / Regulation of thyroid hormone activity / retinal cone cell apoptotic process / brown fat cell proliferation / hormone biosynthetic process / retinal cone cell development / positive regulation of multicellular organism growth / response to hypoxia / endosome membrane / apoptotic process / plasma membrane
Similarity search - Function
Iodothyronine deiodinase I/III / Iodothyronine deiodinase / Iodothyronine deiodinase, active site / Iodothyronine deiodinase / Iodothyronine deiodinases active site. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thyroxine 5-deiodinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSteegborn, C. / Schweizer, U. / Schlicker, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of mammalian selenocysteine-dependent iodothyronine deiodinase suggests a peroxiredoxin-like catalytic mechanism.
Authors: Schweizer, U. / Schlicker, C. / Braun, D. / Kohrle, J. / Steegborn, C.
History
DepositionJun 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Data collection
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Type III iodothyronine deiodinase


Theoretical massNumber of molelcules
Total (without water)21,6971
Polymers21,6971
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.920, 54.300, 66.610
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 Type III iodothyronine deiodinase / 5DIII / DIOIII / Type 3 DI / Type-III 5'-deiodinase


Mass: 21696.639 Da / Num. of mol.: 1 / Mutation: yes
Source method: isolated from a genetically manipulated source
Details: six N-terminal residues are cloning artifact; three C-terminal residues not visible in electron density
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dio3 / Plasmid: pET151 TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: Q91ZI8, EC: 1.97.1.11
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 20 % PEG 3350, 0.2 M Ammoniumcitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 14304 / Num. obs: 14015 / % possible obs: 96 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0042refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
SHELXphasing
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.07 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.035 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 706 5 %RANDOM
Rwork0.1866 13309 --
obs0.1885 14015 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.08 Å2 / Biso mean: 18 Å2 / Biso min: 4.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2---0.54 Å20 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.9→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 93 1555
Biso mean---22.18 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221500
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9532038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06522.97374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82615226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0551514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211194
X-RAY DIFFRACTIONr_mcbond_it0.9711.5935
X-RAY DIFFRACTIONr_mcangle_it1.79721498
X-RAY DIFFRACTIONr_scbond_it2.7213565
X-RAY DIFFRACTIONr_scangle_it4.2364.5540
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 46 -
Rwork0.186 727 -
all-773 -
obs--72.72 %

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