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PDB | 3GH8 | Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and di-iodotyrosine (DIT)

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Internal ID
64196
PDB Entry ID
3GH8
Title
Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and di-iodotyrosine (DIT)
Authors
Thomas, S.R.,McTamney, P.M.,Adler, J.M.,LaRonde-LeBlanc, N.,Rokita, S.E.
Primary Citation
AuthorsThomas, S.R., McTamney, P.M., Adler, J.M., Laronde-Leblanc, N., Rokita, S.E.
TitleCrystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands.
JournalJ.Biol.Chem., v.284, pp.19659 - 19667, 2009
AbstractView
Pubmed19436071
DOI10.1074/jbc.M109.013458
 
History
Deposition: 2009-03-03Release: 2009-05-12Last Modified: 2011-07-13
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.610.1850.1810.264P 1 21 1
Unit Cell
Length [Å]a50.61b112.57c189.25
Angles [°]alpha90.00beta89.92gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Iodotyrosine dehalogenase 1UNP residues 34-285A, B, C, D, E, F, G, H
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Mus musculusmouseSpodoptera frugiperda
Related PDB Entries
IDDetails
3GB5Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN
3GFDCrystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (MIT)
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
FMNFLAVIN MONONUCLEOTIDEC17H21N4O9P[View][View]
TYI3,5-DIIODOTYROSINEC9H9I2NO3[View][View]
PO4PHOSPHATE IONO4P3[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordOXIDOREDUCTASE
TextIYD, iodide salvage, flavoprotein, di-iodotyrosine, DIT, FMN, Membrane, NADP, Oxidoreductase, Transmembrane
 
Polymeric Molecules
Chain A
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Chain B
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Chain C
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Chain D
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Chain E
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Chain F
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Chain G
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Chain H
DescriptionIodotyrosine dehalogenase 1
FragmentUNP residues 34-285
Polymer typepolypeptide
Formula Weight29987.6
Source Methodgenetically manipulated
Entity NameIYD-1
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,B,C,D,E,F,G,Hpolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
FMNFLAVIN MONONUCLEOTIDEC17H21N4O9P456.348View
TYI3,5-DIIODOTYROSINEC9H9I2NO3432.984View
PO4PHOSPHATE IONO4P394.971View
Natural/Genetically Modified Source
Common Namemouse
Scientific NameMus musculus
Source Genusn/a
GeneDehal1, Iyd
Host Common Namen/a
Host Scientific NameSpodoptera frugiperda
Host Genusn/a
Host Cell LineSF9
Host Strainn/a
Host Vector Typeplasmid
Host PlasmidpFASTBAC1
 
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH5.5
Temperature293.0
Details0.2M Ammonium acetate, 45% 2-Methyl-2,4-pentanediol, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
50.61112.57189.25
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0089.9290.00
Space Group
P 1 21 1
Diffraction Detector
DetectorCCD
TypeADSC QUANTUM 315r
Detailsn/a
Collection Date2008-04-04
 
Diffraction Radiation
MonochromatorKohzu HLD8-24
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.9795
 
Diffraction Source
SourceSYNCHROTRON
TypeAPS BEAMLINE 24-ID-C
SiteAPS
Beamline24-ID-C
 
Reflection Details
Observed Criterion Sigma (F)n/a
Observed Criterion Sigma (I)2.0
Resolution (High)2.60
Resolution (Low)50.00
Number Reflections (All) 62935
Number Reflections (Observed)62878
Percent Possible (Observed)97.1
R Merge I (Observed)0.086
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy2.6
 
High Resolution Shell Details
Resolution(High)2.60
Resolution(Low)2.69
Percent Possible(All) 92.90
R Merge I(Observed)n/a
Mean I Over Sigma(Observed)2.4
R Sym I(Observed)0.295
Redundancy2.5
Num Unique Reflections(All)5984
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)2.61
Resolution (Low)30.00
Cut-off Sigma (F)0.0
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)62878
Number of Reflections (R-Free) 3202
Percent Reflections (Observed)96.82
R-Factor (All)0.185
R-Factor (Observed)0.185
R-Work0.181
R-Free0.264
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value35.532
Anisotropic B[1][1]-1.13
Anisotropic B[1][2]0.00
Anisotropic B[1][3]-0.16
Anisotropic B[2][2]-4.05
Anisotropic B[2][3]0.00
Anisotropic B[3][3]5.19
 
Resolution Shells
Shell Resol (High)2.61
Shell Resolution (Low)n/a
Number of Reflections (Observed)4034
Number of Reflections (R-Free)210
Number of Reflections (R-Work)4034
R-Factor (R-Work)0.274
R-Factor (R-Free)0.342
R-Free Errorn/a
Percent Reflections (Observed)88.31
 
RMS Deviations
Parameter TypeDeviation From Ideal
r_bond_refined_d0.019
r_angle_refined_deg1.926
r_dihedral_angle_1_deg7.360
r_dihedral_angle_2_deg37.104
r_dihedral_angle_3_deg20.523
r_dihedral_angle_4_deg19.877
r_chiral_restr0.137
r_gen_planes_refined0.008
r_nbd_refined0.251
r_nbtor_refined0.324
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.206
r_symmetry_hbond_refined0.110
r_mcbond_it0.832
r_mcangle_it1.502
r_scbond_it2.338
r_scangle_it3.693
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms14232
Nucleic Acid Atoms0
Heterogen Atoms378
Solvent Atoms300
 
Programs
Data CollectionHKL-2000
Data Reduction (intensity integration)HKL-2000
Data Reduction (data scaling)HKL-2000
Structure SolutionMOLREP
Structure RefinementREFMAC 5.2.0019
 
Software
Classificationrefinement
Software NameREFMAC5
Software Version 5.2.0019
 
Classificationdata extraction
Software Namepdb_extract
Software Version 3.006
 
Sequence Chain
A
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH  

Sequence Chain
B
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH  

Sequence Chain
C
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH  

Sequence Chain
D
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH  

Sequence Chain
E
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH  

Sequence Chain
F
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH  

Sequence Chain
G
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH  

Sequence Chain
H
Sequence
  1   MAQVQPWVDE  DLKDSTEDLQ  VEEDAEEWQE  AEESVEHIPF  SHTRYPEQEM  RMRSQEFYEL

 61   LNKRRSVRFI  SSEHVPMEVI  ENVIKAAGTA  PSGAHTEPWT  FVVVKDPDMK  HKIREIIEEE

121   EEINYMKRMG  KRWVTDLKKL  RTNWIKEYLD  TAPVLILIFK  QVHGFAANGK  KKVHYYNEIS

181   VSIACGLLLA  ALQNAGLVTV  TTTPLNCGPR  LRVLLGRPSH  EKLLVLLPVG  YPSRDATVPD

241   LKRKALDQIM  VTVHHHHHH