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- PDB-5ko8: Crystal structure of haliscomenobacter hydrossis iodotyrosine dei... -

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Basic information

Entry
Database: PDB / ID: 5ko8
TitleCrystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN and mono-iodotyrosine (I-Tyr)
ComponentsNitroreductase
KeywordsOXIDOREDUCTASE / Haliscomenobacter hydrossis / iodotyrosine deiodinase / flavin mononucleotide
Function / homology
Function and homology information


iodotyrosine deiodinase / iodotyrosine deiodinase activity / FMN binding
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
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsIngavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S.E.
CitationJournal: Biochemistry / Year: 2017
Title: Active Site Binding Is Not Sufficient for Reductive Deiodination by Iodotyrosine Deiodinase.
Authors: Ingavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S.E.
History
DepositionJun 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Data collection / Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitroreductase
B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8596
Polymers52,3322
Non-polymers1,5274
Water2,306128
1
A: Nitroreductase
hetero molecules

A: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8596
Polymers52,3322
Non-polymers1,5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area12280 Å2
ΔGint-80 kcal/mol
Surface area18230 Å2
MethodPISA
2
B: Nitroreductase
hetero molecules

B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8596
Polymers52,3322
Non-polymers1,5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area12390 Å2
ΔGint-77 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.718, 152.718, 87.286
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Nitroreductase /


Mass: 26165.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliscomenobacter hydrossis (strain ATCC 27775 / DSM 1100 / LMG 10767 / O) (bacteria)
Strain: ATCC 27775 / DSM 1100 / LMG 10767 / O / Gene: Halhy_2296 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: F4KU78
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#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 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 150 mM MgCl2, 25% (w/v) PEG 3350, 2 mM I-Tyr and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→38.18 Å / Num. obs: 33077 / % possible obs: 99.9 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GB5

3gb5


Resolution: 2.15→38.18 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1647 4.99 %
Rwork0.1905 --
obs0.1926 33034 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 90 128 3699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053702
X-RAY DIFFRACTIONf_angle_d0.8425049
X-RAY DIFFRACTIONf_dihedral_angle_d13.5141353
X-RAY DIFFRACTIONf_chiral_restr0.032531
X-RAY DIFFRACTIONf_plane_restr0.004647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21330.35311230.30042565X-RAY DIFFRACTION100
2.2133-2.28470.29961340.26642578X-RAY DIFFRACTION100
2.2847-2.36640.29451300.2582560X-RAY DIFFRACTION100
2.3664-2.46110.30081480.26512561X-RAY DIFFRACTION100
2.4611-2.57310.34261490.24052568X-RAY DIFFRACTION100
2.5731-2.70870.25721290.22062592X-RAY DIFFRACTION100
2.7087-2.87840.28481250.21272599X-RAY DIFFRACTION100
2.8784-3.10050.28811260.21992626X-RAY DIFFRACTION100
3.1005-3.41240.27181320.2012619X-RAY DIFFRACTION100
3.4124-3.90570.22651530.17892628X-RAY DIFFRACTION100
3.9057-4.91910.17731520.1472667X-RAY DIFFRACTION100
4.9191-38.18560.18421460.16392824X-RAY DIFFRACTION100

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