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

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Basic information

Entry
Database: PDB / ID: 5krd
TitleCrystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN and 2-iodophenol (2IP)
ComponentsNitroreductase
KeywordsOXIDOREDUCTASE
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
2-iodanylphenol / FLAVIN MONONUCLEOTIDE / Iodotyrosine deiodinase
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsIngavat, N. / Kavran, J.M. / Sun, Z. / Rokita, S.
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
DepositionJul 7, 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 1.3Oct 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)53,6856
Polymers52,3322
Non-polymers1,3534
Water2,270126
1
A: Nitroreductase
hetero molecules

A: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6856
Polymers52,3322
Non-polymers1,3534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area11320 Å2
ΔGint-77 kcal/mol
Surface area17570 Å2
MethodPISA
2
B: Nitroreductase
hetero molecules

B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6856
Polymers52,3322
Non-polymers1,3534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area11370 Å2
ΔGint-75 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.049, 155.049, 89.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21B-415-

HOH

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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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F4KU78
#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-6X8 / 2-iodanylphenol


Mass: 220.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5IO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Tris-HCl pH 9, 200 mM MgCl2, 2 mM 2-iodophenol, 17% (w/v) PEG 8000, 17% glycerol and 10% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 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: 2.1→20 Å / Num. obs: 36524 / % possible obs: 98.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.7

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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: 2.103→19.994 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 1821 5 %
Rwork0.1767 --
obs0.179 36430 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 78 126 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143395
X-RAY DIFFRACTIONf_angle_d1.3864625
X-RAY DIFFRACTIONf_dihedral_angle_d15.4861249
X-RAY DIFFRACTIONf_chiral_restr0.056495
X-RAY DIFFRACTIONf_plane_restr0.007590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1027-2.15950.35751350.31892544X-RAY DIFFRACTION96
2.1595-2.2230.3371350.292646X-RAY DIFFRACTION100
2.223-2.29460.28651380.25442656X-RAY DIFFRACTION100
2.2946-2.37650.27141330.24182659X-RAY DIFFRACTION100
2.3765-2.47150.27951430.22992663X-RAY DIFFRACTION100
2.4715-2.58380.2781470.22032549X-RAY DIFFRACTION96
2.5838-2.71970.2281350.19992679X-RAY DIFFRACTION100
2.7197-2.88960.24541390.18792691X-RAY DIFFRACTION100
2.8896-3.1120.25421230.18452702X-RAY DIFFRACTION100
3.112-3.42370.20851280.17872623X-RAY DIFFRACTION96
3.4237-3.91590.20431580.15582701X-RAY DIFFRACTION100
3.9159-4.92140.18321540.1442652X-RAY DIFFRACTION96
4.9214-19.99460.20471530.15642844X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -50.0449 Å / Origin y: -31.2175 Å / Origin z: 7.5743 Å
111213212223313233
T0.408 Å20.0049 Å2-0.016 Å2-0.3934 Å20.0054 Å2--0.3807 Å2
L2.5402 °2-0.6032 °20.7445 °2-0.2235 °2-0.1204 °2--0.443 °2
S-0.0943 Å °-0.0504 Å °0.2172 Å °0.027 Å °0.0023 Å °-0.0675 Å °0.0091 Å °0.0963 Å °0.1061 Å °
Refinement TLS groupSelection details: all

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