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- PDB-3gb5: Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) b... -

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Basic information

Entry
Database: PDB / ID: 3gb5
TitleCrystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN
ComponentsIodotyrosine dehalogenase 1
KeywordsOXIDOREDUCTASE / IYD / iodide salvage / flavoprotein / FMN / Membrane / NADP / Transmembrane
Function / homology
Function and homology information


Thyroxine biosynthesis / iodotyrosine deiodinase / iodotyrosine deiodinase activity / thyroid hormone metabolic process / tyrosine metabolic process / cytoplasmic vesicle membrane / FMN binding / 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
ACETATE ION / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Iodotyrosine deiodinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsThomas, S.R. / McTamney, P.M. / Adler, J.M. / LaRonde-LeBlanc, N. / Rokita, S.E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands.
Authors: Thomas, S.R. / McTamney, P.M. / Adler, J.M. / Laronde-Leblanc, N. / Rokita, S.E.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6575
Polymers29,9871
Non-polymers6694
Water2,378132
1
A: Iodotyrosine dehalogenase 1
hetero molecules

A: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,31410
Polymers59,9752
Non-polymers1,3398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area8470 Å2
ΔGint-56.3 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.756, 87.756, 62.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsAUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT IS CONFIRMED BY ULTRACENTRIFUGATION

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Components

#1: Protein Iodotyrosine dehalogenase 1 / IYD-1


Mass: 29987.398 Da / Num. of mol.: 1 / Fragment: UNP residues 34-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Iyd, Dehal1 / Plasmid: pFASTBAC1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9DCX8
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 3000, 0.1 M Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.653 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2008
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.653 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 36382 / Num. obs: 36382 / % possible obs: 99.8 % / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.3 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.764 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 984 5.1 %RANDOM
Rwork0.167 ---
all0.169 19113 --
obs0.169 19113 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.58 Å2 / Biso mean: 32.568 Å2 / Biso min: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 44 132 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221605
X-RAY DIFFRACTIONr_angle_refined_deg1.5692.0062187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.6795194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48523.33366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07915286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9621512
X-RAY DIFFRACTIONr_chiral_restr0.1210.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021186
X-RAY DIFFRACTIONr_nbd_refined0.210.2712
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.226
X-RAY DIFFRACTIONr_mcbond_it1.1211.51015
X-RAY DIFFRACTIONr_mcangle_it1.60621590
X-RAY DIFFRACTIONr_scbond_it2.8033708
X-RAY DIFFRACTIONr_scangle_it4.3264.5597
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 76 -
Rwork0.262 1287 -
all-1363 -
obs--98.2 %
Refinement TLS params.Method: refined / Origin x: 19.5688 Å / Origin y: 45.6643 Å / Origin z: 26.0996 Å
111213212223313233
T-0.0921 Å2-0.0191 Å20.0275 Å2--0.0477 Å2-0.0078 Å2---0.0902 Å2
L1.6419 °2-0.5674 °20.1394 °2-1.3365 °2-0.0079 °2--1.395 °2
S-0.0446 Å °0.2253 Å °0.0897 Å °0.0356 Å °0.021 Å °0.0265 Å °-0.2109 Å °0.0211 Å °0.0236 Å °

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