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

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Basic information

Entry
Database: PDB / ID: 3gfd
TitleCrystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (MIT)
ComponentsIodotyrosine dehalogenase 1
KeywordsOXIDOREDUCTASE / IYD / iodide salvage / flavoprotein / mono-iodotyrosine / MIT / 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 / 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-IODO-TYROSINE / Iodotyrosine deiodinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 26, 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Iodotyrosine dehalogenase 1
B: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7789
Polymers59,9752
Non-polymers1,8037
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-60.4 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.187, 105.187, 162.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Iodotyrosine dehalogenase 1 / IYD-1


Mass: 29987.398 Da / Num. of mol.: 2 / Fragment: UNP residues 34-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dehal1, Iyd / 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.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-IYR / 3-IODO-TYROSINE


Type: L-peptide linking / Mass: 307.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10INO3 / Comment: hormone*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 4.32 Å3/Da / Density % sol: 71.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% PEG 3350, 0.2M MgCl2, pH 7.4, 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: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2008
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 38478 / Num. obs: 38170 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 20
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3783 / Rsym value: 0.439 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GB5

3gb5


Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.463 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1925 5 %RANDOM
Rwork0.144 ---
all0.145 36506 --
obs0.145 36214 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 38.779 Å2 / Biso min: 21.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20.94 Å20 Å2
2--1.88 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 108 540 4198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223782
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.9985128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.3235445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15922.821156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19615686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3851530
X-RAY DIFFRACTIONr_chiral_restr0.1410.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022762
X-RAY DIFFRACTIONr_nbd_refined0.2360.22042
X-RAY DIFFRACTIONr_nbtor_refined0.320.22596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2463
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.217
X-RAY DIFFRACTIONr_mcbond_it0.9471.52255
X-RAY DIFFRACTIONr_mcangle_it1.73623659
X-RAY DIFFRACTIONr_scbond_it3.00231739
X-RAY DIFFRACTIONr_scangle_it5.0264.51469
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 141 -
Rwork0.195 2657 -
all-2798 -
obs--99.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82260.1006-0.28281.565-0.64211.9420.01470.07390.141-0.13830.0380.0333-0.111-0.1064-0.0527-0.1045-0.01240.0069-0.06050.0056-0.1015-50.344124.9173-3.22
20.72370.0482-0.48111.2811-0.40222.4852-0.0145-0.07210.030.10130.0158-0.01180.03590.0032-0.0013-0.0883-0.00650.0021-0.0737-0.0044-0.1048-50.970615.143212.4426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 254
2X-RAY DIFFRACTION2B34 - 253

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