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- PDB-4ttc: Crystal structure of homo sapiens IODOTYROSINE DEIODINASE bound t... -

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Basic information

Entry
Database: PDB / ID: 4ttc
TitleCrystal structure of homo sapiens IODOTYROSINE DEIODINASE bound to FMN and mono-iodotyrosine (MIT)
ComponentsIodotyrosine dehalogenase 1
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / MEMBRANE / TRANSMEMBRANE / DEHALOGENASE / IODIDE SALVAGE / MONO-IODOTYROSINE / MIT
Function / homology
Function and homology information


iodotyrosine deiodinase / iodotyrosine deiodinase activity / Thyroxine biosynthesis / tyrosine metabolic process / thyroid hormone 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsChuenchor, W. / Hu, J. / Rokita, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK084186 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Switch between One- and Two-electron Chemistry of the Human Flavoprotein Iodotyrosine Deiodinase Is Controlled by Substrate.
Authors: Hu, J. / Chuenchor, W. / Rokita, S.E.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,51118
Polymers183,9306
Non-polymers4,58112
Water3,981221
1
A: Iodotyrosine dehalogenase 1
B: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8376
Polymers61,3102
Non-polymers1,5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-78 kcal/mol
Surface area18540 Å2
MethodPISA
2
C: Iodotyrosine dehalogenase 1
D: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8376
Polymers61,3102
Non-polymers1,5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-76 kcal/mol
Surface area18450 Å2
MethodPISA
3
E: Iodotyrosine dehalogenase 1
F: Iodotyrosine dehalogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8376
Polymers61,3102
Non-polymers1,5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-77 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.747, 104.747, 303.338
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Iodotyrosine dehalogenase 1 / IYD-1


Mass: 30655.057 Da / Num. of mol.: 6 / Fragment: UNP residues 32-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IYD, C6orf71, DEHAL1 / Plasmid: pET28-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2(DE3) / References: UniProt: Q6PHW0, EC: 1.22.1.1
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-IYR / 3-IODO-TYROSINE


Type: L-peptide linking / Mass: 307.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H10INO3 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 % / Description: Needle-Shaped Crystal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.15 M sodium acetate, 85 mM Tris-HCl, 25.5 % w/v polyethylene glycol 4,000 and 15 % glycerol
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Single wavelength
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 54565 / Num. obs: 54565 / % possible obs: 100 % / Redundancy: 9.6 % / Rsym value: 0.088 / Net I/σ(I): 27.1
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000202202

Resolution: 2.65→44.858 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 2722 5 %Random selection
Rwork0.1704 ---
obs0.1725 54429 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→44.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10680 0 270 221 11171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811214
X-RAY DIFFRACTIONf_angle_d1.2815228
X-RAY DIFFRACTIONf_dihedral_angle_d14.7434200
X-RAY DIFFRACTIONf_chiral_restr0.0471710
X-RAY DIFFRACTIONf_plane_restr0.0051884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.69660.2631420.19942700X-RAY DIFFRACTION98
2.6966-2.74840.27651470.20232719X-RAY DIFFRACTION100
2.7484-2.80450.27641410.20832703X-RAY DIFFRACTION100
2.8045-2.86550.27451460.20672697X-RAY DIFFRACTION100
2.8655-2.93210.27731430.20322742X-RAY DIFFRACTION100
2.9321-3.00540.27791390.21282733X-RAY DIFFRACTION100
3.0054-3.08670.27581400.19612739X-RAY DIFFRACTION100
3.0867-3.17750.27281450.19832724X-RAY DIFFRACTION100
3.1775-3.280.18611420.18272699X-RAY DIFFRACTION100
3.28-3.39720.29461450.18512719X-RAY DIFFRACTION100
3.3972-3.53320.26331450.1872705X-RAY DIFFRACTION100
3.5332-3.69390.21081450.17652734X-RAY DIFFRACTION100
3.6939-3.88860.20081430.16922731X-RAY DIFFRACTION100
3.8886-4.1320.20911490.16322706X-RAY DIFFRACTION100
4.132-4.45080.17611370.14432733X-RAY DIFFRACTION100
4.4508-4.89820.17661460.12872739X-RAY DIFFRACTION100
4.8982-5.60580.19921430.15652713X-RAY DIFFRACTION100
5.6058-7.05830.15951470.16972731X-RAY DIFFRACTION100
7.0583-44.86450.16131370.15412740X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.0538 Å / Origin y: 109.0423 Å / Origin z: 16.9982 Å
111213212223313233
T0.2034 Å2-0.0193 Å2-0.0128 Å2-0.1416 Å2-0.0688 Å2--0.1453 Å2
L0.034 °20.0226 °2-0.1859 °2-0.4535 °2-0.1158 °2---0.0564 °2
S-0.0576 Å °0.0317 Å °0.0105 Å °0.0538 Å °-0.0693 Å °-0.0081 Å °-0.0077 Å °0.0749 Å °-0.052 Å °
Refinement TLS groupSelection details: all

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