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- PDB-9h48: Mouse Iodothyronine deiodinase 2 catalytic core, mutant - LysLys1... -

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Basic information

Entry
Database: PDB / ID: 9h48
TitleMouse Iodothyronine deiodinase 2 catalytic core, mutant - LysLys180AlaAla, Secys-> Cys
ComponentsType II iodothyronine deiodinase
KeywordsOXIDOREDUCTASE / Thioredoxin-fold / iodothyronine deiodinase
Function / homology
Function and homology information


thyroxine 5'-deiodinase / : / thyroxine 5'-deiodinase activity / thyroid hormone catabolic process / Regulation of thyroid hormone activity / thyroid-stimulating hormone secretion / hormone biosynthetic process / brown fat cell differentiation / positive regulation of cold-induced thermogenesis / plasma membrane
Similarity search - Function
Iodothyronine deiodinase / Iodothyronine deiodinase, active site / Iodothyronine deiodinase / Iodothyronine deiodinases active site. / Thioredoxin-like superfamily
Similarity search - Domain/homology
Type II iodothyronine deiodinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsTowell, H. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)1701/16-1 (SPP 1629) Germany
CitationJournal: Biomolecules / Year: 2024
Title: Structural Insights into the Iodothyronine Deiodinase 2 Catalytic Core and Deiodinase Catalysis and Dimerization.
Authors: Towell, H. / Braun, D. / Brol, A. / di Fonzo, A. / Rijntjes, E. / Kohrle, J. / Schweizer, U. / Steegborn, C.
History
DepositionOct 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II iodothyronine deiodinase


Theoretical massNumber of molelcules
Total (without water)21,3481
Polymers21,3481
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.772, 47.772, 64.686
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Type II iodothyronine deiodinase / 5DII / DIOII / Type 2 DI / Type-II 5'-deiodinase


Mass: 21347.764 Da / Num. of mol.: 1 / Mutation: K180A, K181A, U126C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dio2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z1Y9, thyroxine 5'-deiodinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG buffer pH 7.0, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.089→34.85 Å / Num. obs: 65565 / % possible obs: 94.85 % / Redundancy: 5.4 % / Biso Wilson estimate: 14.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0694 / Rrim(I) all: 0.07659 / Net I/σ(I): 9.45
Reflection shellResolution: 1.089→1.128 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.39 / Num. unique obs: 4435 / CC1/2: 0.117 / % possible all: 64.62

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TR3

4tr3


Resolution: 1.09→34.85 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1694 2098 3.2 %
Rwork0.1451 63458 -
obs0.1459 65556 94.85 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.19 Å2
Refinement stepCycle: LAST / Resolution: 1.09→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1425 0 0 192 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01481507
X-RAY DIFFRACTIONf_angle_d1.44952058
X-RAY DIFFRACTIONf_chiral_restr0.1071221
X-RAY DIFFRACTIONf_plane_restr0.0131279
X-RAY DIFFRACTIONf_dihedral_angle_d5.4665212
LS refinement shellResolution: 1.09→1.11 Å
RfactorNum. reflection% reflection
Rfree0.3875 89 -
Rwork0.3794 2712 -
obs--61.1 %

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