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- PDB-6q1b: Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound... -

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Basic information

Entry
Database: PDB / ID: 6q1b
TitleCrystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and 3-fluoro-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-FLUOROTYROSINE / Iodotyrosine deiodinase
Similarity search - Component
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.596 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: To Be Published
Title: Crystal structure of oxidized Tn IYD bound to FMN and 3-fluoro-L-tyrosine
Authors: Sun, Z. / Kavran, J.M. / Rokita, S.E.
History
DepositionAug 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,27411
Polymers45,7852
Non-polymers1,4889
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-107 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.305, 80.772, 102.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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, iodotyrosine deiodinase
#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-YOF / 3-FLUOROTYROSINE


Type: L-peptide linking / Mass: 199.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10FNO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 407 / 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: 1.99 Å3/Da / Density % sol: 38.27 %
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 PILATUS 6M / Detector: PIXEL / Date: May 6, 2019
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: 1.596→39.08 Å / Num. obs: 47254 / % possible obs: 99.6 % / Redundancy: 26.1 % / Biso Wilson estimate: 17.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.026 / Rrim(I) all: 0.133 / Net I/σ(I): 17
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
1.6-1.6222.71.6184916221620.8830.3321.6532.193.2
8.74-39.0823.80.06884773560.9990.0140.0693499.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.596→37.554 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.93
RfactorNum. reflection% reflection
Rfree0.2032 2382 5.05 %
Rwork0.1657 --
obs0.1676 47170 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 209.19 Å2 / Biso mean: 26.8259 Å2 / Biso min: 9.01 Å2
Refinement stepCycle: final / Resolution: 1.596→37.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 133 407 3629
Biso mean--14.65 37.13 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153298
X-RAY DIFFRACTIONf_angle_d1.3934479
X-RAY DIFFRACTIONf_chiral_restr0.058467
X-RAY DIFFRACTIONf_plane_restr0.007560
X-RAY DIFFRACTIONf_dihedral_angle_d12.8451297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.596-1.62810.45431240.4012247394
1.6281-1.66350.32991320.29252572100
1.6635-1.70220.30321320.22182629100
1.7022-1.74480.23691440.1932583100
1.7448-1.79190.22841340.18342614100
1.7919-1.84470.20871450.18722619100
1.8447-1.90420.23291540.18982597100
1.9042-1.97230.2291510.17772615100
1.9723-2.05120.21661180.16122620100
2.0512-2.14460.21831210.15772653100
2.1446-2.25760.18411490.14532632100
2.2576-2.3990.17811410.162636100
2.399-2.58420.25371600.17072642100
2.5842-2.84420.19971380.17732658100
2.8442-3.25560.19521420.16382703100
3.2556-4.10090.17041390.12832698100
4.1009-37.5540.16031580.14812844100
Refinement TLS params.Method: refined / Origin x: -5.7218 Å / Origin y: -3.4097 Å / Origin z: 6.9105 Å
111213212223313233
T0.112 Å2-0.0045 Å2-0.0034 Å2-0.1177 Å2-0.0048 Å2--0.1082 Å2
L0.553 °2-0.0725 °20.0457 °2-0.5398 °2-0.3831 °2--0.5644 °2
S-0.0081 Å °0.0205 Å °-0.0262 Å °-0.0144 Å °0.0192 Å °0.0153 Å °0.0071 Å °-0.0198 Å °-0.0145 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 301
2X-RAY DIFFRACTION1allA502
3X-RAY DIFFRACTION1allB3 - 301
4X-RAY DIFFRACTION1allB502
5X-RAY DIFFRACTION1allC2 - 5
6X-RAY DIFFRACTION1allC6
7X-RAY DIFFRACTION1allS1 - 419

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