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- PDB-5ko7: Crystal structure of haliscomenobacter hydrossis iodotyrosine dei... -

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Basic information

Entry
Database: PDB / ID: 5ko7
TitleCrystal structure of haliscomenobacter hydrossis iodotyrosine deiodinase (IYD) bound to FMN
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
FLAVIN MONONUCLEOTIDE / Iodotyrosine deiodinase
Similarity search - Component
Biological speciesHaliscomenobacter hydrossis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 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
DepositionJun 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: 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)53,2454
Polymers52,3322
Non-polymers9132
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11110 Å2
ΔGint-73 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.185, 110.881, 43.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-436-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 80 mM Tris-HCl pH 8.5, 100 mM MgCl2, 24% (w/v) PEG 4000 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.248→36.96 Å / Num. obs: 21635 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2

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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: 2.248→35.443 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 1115 5.19 %
Rwork0.2157 --
obs0.2176 21476 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.248→35.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 62 62 3340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033382
X-RAY DIFFRACTIONf_angle_d0.7074608
X-RAY DIFFRACTIONf_dihedral_angle_d13.941254
X-RAY DIFFRACTIONf_chiral_restr0.029496
X-RAY DIFFRACTIONf_plane_restr0.003588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.248-2.35020.47211290.38662211X-RAY DIFFRACTION88
2.3502-2.47410.36731480.32742530X-RAY DIFFRACTION99
2.4741-2.62910.35071290.28462551X-RAY DIFFRACTION100
2.6291-2.8320.29361300.27712552X-RAY DIFFRACTION100
2.832-3.11680.33251500.25872550X-RAY DIFFRACTION100
3.1168-3.56750.28171340.22952592X-RAY DIFFRACTION100
3.5675-4.49320.19321470.18052614X-RAY DIFFRACTION100
4.4932-35.44750.19871480.16552761X-RAY DIFFRACTION100

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