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- PDB-3gh8: Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) b... -

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Basic information

Entry
Database: PDB / ID: 3gh8
TitleCrystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and di-iodotyrosine (DIT)
ComponentsIodotyrosine dehalogenase 1
KeywordsOXIDOREDUCTASE / IYD / iodide salvage / flavoprotein / di-iodotyrosine / DIT / 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
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / 3,5-DIIODOTYROSINE / Iodotyrosine deiodinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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
DepositionMar 3, 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
C: Iodotyrosine dehalogenase 1
D: Iodotyrosine dehalogenase 1
E: Iodotyrosine dehalogenase 1
F: Iodotyrosine dehalogenase 1
G: Iodotyrosine dehalogenase 1
H: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,20426
Polymers239,8998
Non-polymers7,30518
Water5,405300
1
A: Iodotyrosine dehalogenase 1
B: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7536
Polymers59,9752
Non-polymers1,7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-58.9 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: Iodotyrosine dehalogenase 1
D: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8487
Polymers59,9752
Non-polymers1,8745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-57.7 kcal/mol
Surface area19270 Å2
MethodPISA
3
E: Iodotyrosine dehalogenase 1
F: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7536
Polymers59,9752
Non-polymers1,7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-59.6 kcal/mol
Surface area19210 Å2
MethodPISA
4
G: Iodotyrosine dehalogenase 1
H: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8487
Polymers59,9752
Non-polymers1,8745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-59.9 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 112.567, 189.253
Angle α, β, γ (deg.)90.000, 89.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Iodotyrosine dehalogenase 1 / IYD-1


Mass: 29987.398 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-TYI / 3,5-DIIODOTYROSINE


Type: L-peptide linking / Mass: 432.982 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H9I2NO3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium acetate, 45% 2-Methyl-2,4-pentanediol, 0.1M Bis-Tris pH 5.5, 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: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2008
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 62935 / Num. obs: 62878 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 9.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5984 / Rsym value: 0.295 / % possible all: 92.9

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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: 2.61→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.028 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 9.88 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The chirality errors and angles outside Ramachandran plot are due to poor density in flexible regions.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3202 5.1 %RANDOM
Rwork0.181 ---
all0.185 ---
obs0.185 62878 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.41 Å2 / Biso mean: 35.532 Å2 / Biso min: 8.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å2-0.16 Å2
2---4.05 Å20 Å2
3---5.19 Å2
Refinement stepCycle: LAST / Resolution: 2.61→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14232 0 378 300 14910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02214942
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.99920278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3651756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10422.958622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.523152708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.87715120
X-RAY DIFFRACTIONr_chiral_restr0.1370.22276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210932
X-RAY DIFFRACTIONr_nbd_refined0.2510.27345
X-RAY DIFFRACTIONr_nbtor_refined0.3240.210127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2672
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.26
X-RAY DIFFRACTIONr_mcbond_it0.8321.58961
X-RAY DIFFRACTIONr_mcangle_it1.502214496
X-RAY DIFFRACTIONr_scbond_it2.33836915
X-RAY DIFFRACTIONr_scangle_it3.6934.55782
LS refinement shellResolution: 2.61→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 210 -
Rwork0.274 4034 -
all-4244 -
obs-4034 88.31 %
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)
10.5962-0.2301-0.17072.3901-0.11230.73120.02260.0640.0399-0.33860.03040.2127-0.1382-0.1063-0.053-0.0177-0.0018-0.0403-0.09050.0157-0.086-5.71543.029299.8262
20.54490.02730.00692.4472-0.52560.8646-0.0458-0.1103-0.0762-0.10120.0417-0.12840.10430.0770.004-0.0654-0.00420.0281-0.089-0.0147-0.0562.119-12.1064107.0563
31.3235-0.5121-0.20152.81390.44450.4344-0.00180.1664-0.24210.0406-0.10590.36980.0145-0.05950.1077-0.13770-0.0004-0.0773-0.04410.009513.9248-1.796846.3137
40.9971-0.2758-0.38262.4470.81240.97210.0568-0.14920.15330.26090.0202-0.1864-0.03270.122-0.077-0.066-0.0117-0.0405-0.0615-0.0357-0.099721.57312.289355.6683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 254
2X-RAY DIFFRACTION2B36 - 254
3X-RAY DIFFRACTION3C36 - 254
4X-RAY DIFFRACTION4D39 - 254

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