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- PDB-4xdg: Crystal Structure of Quinone Reductase II in complex with 2-(4-am... -

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Basic information

Entry
Database: PDB / ID: 4xdg
TitleCrystal Structure of Quinone Reductase II in complex with 2-(4-aminophenyl)-5-methoxy-1-oxy-indol-3-one molecule
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / QR2 / FAD / FLAVOPROTEIN / METAL-BINDING / indolone oxide
Function / homology
Function and homology information


ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / electron transfer activity / oxidoreductase activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3ZU / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSirigu, S. / Nepveu, F. / Vuillard, L. / Ferry, G. / Isabet, T. / Thompson, A. / Boutin, J.A.
CitationJournal: Molecules / Year: 2017
Title: Role of Quinone Reductase 2 in the Antimalarial Properties of Indolone-Type Derivatives.
Authors: Cassagnes, L.E. / Rakotoarivelo, N. / Sirigu, S. / Perio, P. / Najahi, E. / Chavas, L.M. / Thompson, A. / Gayon, R. / Ferry, G. / Boutin, J.A. / Valentin, A. / Reybier, K. / Nepveu, F.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2May 8, 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

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Assembly

Deposited unit
A: Ribosyldihydronicotinamide dehydrogenase [quinone]
B: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,48811
Polymers51,9612
Non-polymers2,5279
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-72 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.480, 83.630, 106.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ribosyldihydronicotinamide dehydrogenase [quinone] / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone reductase 2 / QR2


Mass: 25980.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P16083, EC: 1.10.99.2

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Non-polymers , 5 types, 533 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-3ZU / (2S)-2-(4-aminophenyl)-1-hydroxy-5-methoxy-1,2-dihydro-3H-indol-3-one


Mass: 268.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12N2O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.4M Ammonium Sulphate; 100 mM Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
RadiationMonochromator: chanel cut Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 81302 / % possible obs: 99.9 % / Redundancy: 7.31 % / Biso Wilson estimate: 17.62 Å2 / Rsym value: 0.009 / Net I/σ(I): 12.58
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 7.14 % / Mean I/σ(I) obs: 3.11 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.81 Å / Cor.coef. Fo:Fc: 0.9631 / Cor.coef. Fo:Fc free: 0.9592 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.069 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 4066 5 %RANDOM
Rwork0.1663 ---
obs0.1673 81302 99.94 %-
Displacement parametersBiso mean: 26.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.4677 Å20 Å20 Å2
2---1.024 Å20 Å2
3---3.4918 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: 1 / Resolution: 1.5→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 163 524 4414
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014007HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025474HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1327SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes697HARMONIC5
X-RAY DIFFRACTIONt_it4007HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.18
X-RAY DIFFRACTIONt_other_torsion15.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion499SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5333SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2835 297 5.01 %
Rwork0.2398 5632 -
all0.2419 5929 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3209-0.1422-0.55270.43270.65113.87060.10580.05510.0336-0.1687-0.0126-0.0451-0.5442-0.129-0.0933-0.00140.02990.0264-0.15190.0002-0.119612.64618.96154.2695
20.2316-0.0586-0.11160.92240.40021.90250.0242-0.0496-0.0081-0.00840.02680.0084-0.16590.0152-0.0509-0.02010.00820.0131-0.07280.0058-0.05539.39857.795326.4392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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