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

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Basic information

Entry
Database: PDB / ID: 4xdh
TitleCrystal Structure of Quinone Reductase II in complex with a 2-(4-methoxy-phenyl)-5-methoxy-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
5-methoxy-2-(4-methoxyphenyl)-3H-indol-3-one / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)54,48611
Polymers51,9612
Non-polymers2,5259
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-72 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.510, 84.030, 106.420
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] / quinone reductase II / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone ...quinone reductase II / 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, 264 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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-3ZV / 5-methoxy-2-(4-methoxyphenyl)-3H-indol-3-one


Mass: 267.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.6M Ammonium Sulphate, 100 mM Bicine pH8

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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: Oct 15, 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: 1.9→50 Å / Num. obs: 40641 / % possible obs: 99.4 % / Redundancy: 7.32 % / Biso Wilson estimate: 26.56 Å2 / Rsym value: 0.02 / Net I/σ(I): 6.83
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 7.34 % / Mean I/σ(I) obs: 1.61 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.82 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.9365 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 2032 5 %RANDOM
Rwork0.1709 ---
obs0.1723 40641 99.94 %-
Displacement parametersBiso mean: 32.17 Å2
Baniso -1Baniso -2Baniso -3
1--5.7626 Å20 Å20 Å2
2---2.7408 Å20 Å2
3---8.5034 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: 1 / Resolution: 1.9→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 163 255 4053
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013907HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995329HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1293SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes675HARMONIC5
X-RAY DIFFRACTIONt_it3907HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion16.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion487SEMIHARMONIC5
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_contact4782SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2313 148 4.98 %
Rwork0.2241 2822 -
all0.2244 2970 -
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)
10.4628-0.20240.65170.7618-0.3753.31020.08860.0721-0.0772-0.1411-0.00810.05030.45950.1547-0.0804-0.01540.0258-0.0154-0.168-0.0055-0.0946-11.9875-8.5384.1928
20.3434-0.07780.16251.0204-0.18471.79930.0282-0.0569-0.00840.02390.011-0.01070.1685-0.0209-0.0393-0.02030.0035-0.0078-0.10380.0012-0.0494-9.9828-8.019826.5157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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