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- PDB-4tr4: Mouse iodothyronine deiodinase 3 catalytic core, active site muta... -

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Basic information

Entry
Database: PDB / ID: 4tr4
TitleMouse iodothyronine deiodinase 3 catalytic core, active site mutant SeCys->Cys
ComponentsType III iodothyronine deiodinase
KeywordsOXIDOREDUCTASE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.93 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 1.1Dec 20, 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

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Assembly

Deposited unit
A: Type III iodothyronine deiodinase


Theoretical massNumber of molelcules
Total (without water)21,5091
Polymers21,5091
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.807, 54.188, 66.493
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: 21509.061 Da / Num. of mol.: 1 / Fragment: Residues 120-304 / Mutation: SeCys170Cys
Source method: isolated from a genetically manipulated source
Details: 6 residue cloning artifact at the N-terminus, 3 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.: 114 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20 % PEG 3350, 0.2 M Ammoniumcitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 13799 / % possible obs: 98.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.086 / Χ2: 1.138 / Net I/σ(I): 11.9 / Num. measured all: 77104
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.93-20.34812141.17789.5
2-2.0850.313031.14896.5
2.08-2.175.60.25113451.26599.1
2.17-2.295.90.22513631.211100
2.29-2.4360.19813631.242100
2.43-2.6260.16413631.189100
2.62-2.8860.13313871.184100
2.88-3.360.09213901.044100
3.3-4.165.90.0714100.938100
4.16-505.60.04915031.01799.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0042refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tr3

4tr3


Resolution: 1.93→42 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 3.278 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 680 5 %RANDOM
Rwork0.1912 12919 --
obs0.1933 13599 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.14 Å2 / Biso mean: 16.364 Å2 / Biso min: 3.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 1.93→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 0 114 1575
Biso mean---19.02 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221499
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9522038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42823.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1761514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211198
X-RAY DIFFRACTIONr_mcbond_it0.9861.5935
X-RAY DIFFRACTIONr_mcangle_it1.73921497
X-RAY DIFFRACTIONr_scbond_it2.413564
X-RAY DIFFRACTIONr_scangle_it3.8034.5541
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 45 -
Rwork0.186 835 -
all-880 -
obs--88 %

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