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- PDB-3tnz: Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) C... -

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Basic information

Entry
Database: PDB / ID: 3tnz
TitleCrystal structure of Mus musculus iodotyrosine deiodinase (IYD) C217A, C239A bound to FMN and mono-iodotyrosine (MIT)
ComponentsIodotyrosine dehalogenase 1
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / MEMBRANE / TRANSMEMBRANE / DEHALOGENASE / IODIDE SALVAGE / FMN / MONO-IODOTYROSINE / MIT / NADP
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
CITRATE ANION / FLAVIN MONONUCLEOTIDE / 3-IODO-TYROSINE / Iodotyrosine deiodinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBuss, J.M. / McTamney, P.M. / Rokita, S.E.
CitationJournal: Protein Sci. / Year: 2012
Title: Expression of a soluble form of iodotyrosine deiodinase for active site characterization by engineering the native membrane protein from Mus musculus.
Authors: Buss, J.M. / McTamney, P.M. / Rokita, S.E.
History
DepositionSep 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Sep 13, 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)61,93610
Polymers59,8472
Non-polymers2,0898
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-75 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.986, 108.986, 49.399
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 66:286 )
211chain B and (resseq 66:286 )

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Iodotyrosine dehalogenase 1 / IYD-1


Mass: 29923.273 Da / Num. of mol.: 2 / Mutation: C217A, C239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: 10090 / Gene: Dehal1, Iyd, IYD-1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9DCX8, EC: 1.22.1.1

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Non-polymers , 5 types, 306 molecules

#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
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 10,000, 0.1M citric acid pH 5.0, 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: Jul 1, 2010
RadiationMonochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 31135 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 8 % / Rsym value: 0.15 / Net I/σ(I): 12.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3065 / Rsym value: 0.593 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4Phasermodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4Phaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GFD

3gfd


Resolution: 2.25→26.537 Å / SU ML: 0.72 / σ(F): 1.96 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 1567 5.04 %RANDOM
Rwork0.1706 ---
obs0.1721 31094 99.57 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.381 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0042 Å2-0 Å20 Å2
2---0.0042 Å20 Å2
3---0.0085 Å2
Refinement stepCycle: LAST / Resolution: 2.25→26.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 128 298 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143790
X-RAY DIFFRACTIONf_angle_d1.3845142
X-RAY DIFFRACTIONf_dihedral_angle_d15.6271456
X-RAY DIFFRACTIONf_chiral_restr0.084572
X-RAY DIFFRACTIONf_plane_restr0.007638
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1773X-RAY DIFFRACTIONPOSITIONAL
12B1773X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.32060.33751230.27212601X-RAY DIFFRACTION96
2.3206-2.40350.25731320.24042704X-RAY DIFFRACTION100
2.4035-2.49970.27811420.20232716X-RAY DIFFRACTION100
2.4997-2.61330.2511540.20572654X-RAY DIFFRACTION100
2.6133-2.7510.22421450.16012702X-RAY DIFFRACTION100
2.751-2.92310.17871590.16922691X-RAY DIFFRACTION100
2.9231-3.14850.21521490.16162685X-RAY DIFFRACTION100
3.1485-3.46470.19121230.16352705X-RAY DIFFRACTION100
3.4647-3.96460.18011380.15292686X-RAY DIFFRACTION100
3.9646-4.98960.14771610.1242704X-RAY DIFFRACTION100
4.9896-26.53840.18731410.17952679X-RAY DIFFRACTION100
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)
11.2147-0.2910.04710.7651-0.02970.82530.040.0401-0.0838-0.0469-0.0012-0.03830.02730.0983-0.03820.13410.0365-0.00770.1675-0.0060.14439.5607-9.95428.4838
21.1057-0.3968-0.00880.93930.05890.76970.0114-0.0683-0.03460.02880.01390.0876-0.0615-0.0712-0.02610.12510.0307-0.00440.17460.00840.140825.9248-2.158414.4572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 66:287)
2X-RAY DIFFRACTION2chain 'B' and (resseq 66:286)

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