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- PDB-6q1l: Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound... -

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Basic information

Entry
Database: PDB / ID: 6q1l
TitleCrystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and 3-iodo-L-tyrosine
Componentsiodotyrosine deiodinase
KeywordsOXIDOREDUCTASE / flavoprotein / dehalogenase / thermophile / halotyrosine
Function / homology
Function and homology information


L-tyrosine binding / iodotyrosine deiodinase / iodotyrosine deiodinase activity / tyrosine metabolic process / FMN binding
Similarity search - Function
Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 3-IODO-TYROSINE / Iodotyrosine deiodinase
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSun, Z. / Kavran, J.M. / Rokita, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana.
Authors: Sun, Z. / Xu, B. / Spisak, S. / Kavran, J.M. / Rokita, S.E.
History
DepositionAug 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 20, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / database_2 / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _database_2.pdbx_DOI ..._cell.volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _pdbx_contact_author.id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _symmetry.space_group_name_Hall
Description: Model completeness / Details: refined occupancy of I-Tyr ligands / Provider: author / Type: Coordinate replacement
Revision 2.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iodotyrosine deiodinase
B: iodotyrosine deiodinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,52512
Polymers45,7852
Non-polymers1,74010
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-121 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.861, 81.232, 103.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein iodotyrosine deiodinase / / IYD


Mass: 22892.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NS-E) (bacteria)
Strain: ATCC 49049 / DSM 4359 / NS-E / Gene: CTN_0569 / Production host: Escherichia coli (E. coli) / References: UniProt: B9K712
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IYR / 3-IODO-TYROSINE / 3-Iodotyrosine


Type: L-peptide linking / Mass: 307.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10INO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium citrate, pH 4.5, 3 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.598→37.91 Å / Num. obs: 47126 / % possible obs: 96.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.039 / Rrim(I) all: 0.086 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.634.20.737948422640.8010.380.8332.195.5
8.75-37.914.60.05714523160.9970.0290.06523.590.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→37.91 Å / SU ML: 0.1365 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2027 2334 4.96 %
Rwork0.1705 44732 -
obs0.1721 47066 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 96 314 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013289
X-RAY DIFFRACTIONf_angle_d1.12674468
X-RAY DIFFRACTIONf_chiral_restr0.0527466
X-RAY DIFFRACTIONf_plane_restr0.0072559
X-RAY DIFFRACTIONf_dihedral_angle_d12.59091292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.26211460.23332574X-RAY DIFFRACTION95.91
1.63-1.670.26081350.21942663X-RAY DIFFRACTION99.08
1.67-1.710.25271140.20642680X-RAY DIFFRACTION98.24
1.71-1.750.22131490.1992597X-RAY DIFFRACTION97.93
1.75-1.790.2471290.20082638X-RAY DIFFRACTION97.05
1.79-1.850.21711330.19072652X-RAY DIFFRACTION97.55
1.85-1.910.2291360.18422629X-RAY DIFFRACTION98.01
1.91-1.980.21011600.18182654X-RAY DIFFRACTION98.12
1.98-2.050.2021550.17522606X-RAY DIFFRACTION97.46
2.05-2.150.22371440.17692632X-RAY DIFFRACTION96.29
2.15-2.260.19781340.16232598X-RAY DIFFRACTION95.79
2.26-2.40.20211110.16672668X-RAY DIFFRACTION96.93
2.4-2.590.17491230.1682638X-RAY DIFFRACTION96.24
2.59-2.850.19521530.17662586X-RAY DIFFRACTION94.22
2.85-3.260.21371380.17592635X-RAY DIFFRACTION95.16
3.26-4.110.1621260.13782603X-RAY DIFFRACTION92.76
4.11-37.910.20021480.16062679X-RAY DIFFRACTION91.11

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