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- PDB-3o73: Crystal structure of quinone reductase 2 in complex with the indo... -

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Basic information

Entry
Database: PDB / ID: 3o73
TitleCrystal structure of quinone reductase 2 in complex with the indolequinone MAC627
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Quinone reductase 2 / NQO2 / Oxidoreductase / Flavoprotein / Indolequinone MAC627 / FAD / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-O73 / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDufour, M. / Yan, C. / Colucci, M.A. / Siegel, D. / Li, Y. / De Matteis, C.I. / Ross, D. / Moody, C.J.
CitationJournal: Chembiochem / Year: 2011
Title: Mechanism-Based Inhibition of Quinone Reductase 2 (NQO2): Selectivity for NQO2 over NQO1 and Structural Basis for Flavoprotein Inhibition.
Authors: Dufour, M. / Yan, C. / Siegel, D. / Colucci, M.A. / Jenner, M. / Oldham, N.J. / Gomez, J. / Reigan, P. / Li, Y. / De Matteis, C.I. / Ross, D. / Moody, C.J.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,1468
Polymers53,6192
Non-polymers2,5276
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-33 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.080, 82.050, 106.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26809.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pMTL1015 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P16083, EC: 1.10.99.2
#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-O73 / 5-[(4-aminobutyl)amino]-1,2-dimethyl-3-[(4-nitrophenoxy)methyl]-1H-indole-4,7-dione


Mass: 412.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N4O5
#5: 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.60M ammonium sulphate, 100mM Na-HEPES pH 7, 12uM FAD, 1mM dithiothreitol, 200uM indolequinone MAC627, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→35.45 Å / Num. all: 28053 / Num. obs: 28053 / % possible obs: 82.3 % / Redundancy: 4.5 % / Rsym value: 0.106 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 4230 / Rsym value: 0.679 / % possible all: 86.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QR2

1qr2


Resolution: 2→35.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28798 1407 5 %RANDOM
Rwork0.22015 ---
obs0.22345 26579 81.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.795 Å2
Baniso -1Baniso -2Baniso -3
1-4.08 Å20 Å20 Å2
2---0.8 Å20 Å2
3----3.28 Å2
Refinement stepCycle: LAST / Resolution: 2→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 168 62 3876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223928
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9945356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75924.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31315612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7761516
X-RAY DIFFRACTIONr_chiral_restr0.1220.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212988
X-RAY DIFFRACTIONr_mcbond_it1.1521.52286
X-RAY DIFFRACTIONr_mcangle_it2.01223682
X-RAY DIFFRACTIONr_scbond_it2.9831642
X-RAY DIFFRACTIONr_scangle_it4.4924.51674
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 110 -
Rwork0.305 2045 -
obs--85.99 %

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