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- PDB-3to0: Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) C... -

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Basic information

Entry
Database: PDB / ID: 3to0
TitleCrystal structure of Mus musculus iodotyrosine deiodinase (IYD) C217A, C239A bound to FMN
ComponentsIodotyrosine deiodinase 1
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / MEMBRANE / TRANSMEMBRANE / DEHALOGENASE / IODIDE SALVAGE / MONO-IODOTYROSINE / NADP
Function / homology
Function and homology information


Thyroxine biosynthesis / iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / thyroid hormone 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 / MOLECULAR REPLACEMENT / Resolution: 2.655 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 deiodinase 1
B: Iodotyrosine deiodinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0678
Polymers59,8472
Non-polymers1,2216
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-66 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.270, 87.270, 62.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 68:155 or resseq 178:194 or resseq 208:286 )
211chain B and (resseq 68:155 or resseq 178:194 or resseq 208:286 )

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Components

#1: Protein Iodotyrosine deiodinase 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: IYD-1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9DCX8, EC: 1.22.1.1
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / 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.: 50 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M ammonium acetate 0.1M Bis-Tris pH 6.0, 45% v/v 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.655→19.88 Å / Num. obs: 15404 / % possible obs: 99.71 % / Redundancy: 3.7 % / Rsym value: 0.105 / Net I/σ(I): 73
Reflection shellResolution: 2.656→2.75 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.81 / Num. unique all: 1493 / Rsym value: 0.534 / % possible all: 80.14

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CCP4Phasermodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
SAINTdata reduction
SADABSdata scaling
CCP4Phaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GB5

3gb5


Resolution: 2.655→19.88 Å / SU ML: 0.95 / σ(F): 1.96 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1367 4.93 %RANDOM
Rwork0.1823 ---
obs0.185 14367 89.94 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.424 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1087 Å20 Å2-0 Å2
2---1.1087 Å2-0 Å2
3----3.6507 Å2
Refinement stepCycle: LAST / Resolution: 2.655→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 80 50 3074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153083
X-RAY DIFFRACTIONf_angle_d1.6394191
X-RAY DIFFRACTIONf_dihedral_angle_d17.2521161
X-RAY DIFFRACTIONf_chiral_restr0.093485
X-RAY DIFFRACTIONf_plane_restr0.006522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1467X-RAY DIFFRACTIONPOSITIONAL
12B1467X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6552-2.750.3519970.34481892X-RAY DIFFRACTION65
2.75-2.860.3747840.3012198X-RAY DIFFRACTION74
2.86-2.990.30241400.25042369X-RAY DIFFRACTION80
2.99-3.14750.28371560.19552534X-RAY DIFFRACTION88
3.1475-3.34440.2361580.17882758X-RAY DIFFRACTION95
3.3444-3.60220.25021500.17522876X-RAY DIFFRACTION98
3.6022-3.96380.19431640.15442956X-RAY DIFFRACTION100
3.9638-4.53540.19451400.13742920X-RAY DIFFRACTION100
4.5354-5.70670.2081400.16132934X-RAY DIFFRACTION100
5.7067-28.56750.2231380.18442941X-RAY DIFFRACTION100
Refinement TLS params.

T13: 0.0027 Å2 / 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)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76870.00460.35841.0404-0.00010.95140.088-0.107-0.06310.0879-0.0434-0.03860.0810.0423-0.00360.097-0.02060.0988-0.00930.10415.41819.0766-5.6206
20.8759-0.0026-0.19591.09910.10191.10250.06320.09510.0671-0.1118-0.0571-0.058-0.05690.07160.02760.0980.01850.0912-0.00730.10025.444231.0542-16.0306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 68:286)
2X-RAY DIFFRACTION2chain 'B' and (resseq 68:287)

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