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- PDB-4zvm: Oxidized quinone reductase 2 in complex with doxorubicin -

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Basic information

Entry
Database: PDB / ID: 4zvm
TitleOxidized quinone reductase 2 in complex with doxorubicin
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
Keywordsoxidoreductase/oxidoreductase inhibitor / quinone reductase 2 / doxorubicin / Oxidoreductase-Inhibitor complex / 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
DOXORUBICIN / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.973 Å
Model detailsMetallo-flavoprotein
AuthorsLeung, K.K. / Shilton, B.H.
CitationJournal: Biochemistry / Year: 2015
Title: Binding of DNA-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2.
Authors: Leung, K.K. / Shilton, B.H.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)54,4888
Polymers51,6992
Non-polymers2,7896
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-19 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.230, 83.340, 106.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 25849.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pProEXhta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H29NO11
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe mismatch between F46 (in the deposited structure) and L47 (from UNP P16083) is due to SNP ...The mismatch between F46 (in the deposited structure) and L47 (from UNP P16083) is due to SNP rs1143684. Both forms of NQO2 are found in the population where F46 is the predominant form in the population. For your reference - 1. Megarity, C. F., Gill, J. R. E., Caraher, M. C., Stratford, I. J., Nolan, K. a, and Timson, D. J. (2014) The two common polymorphic forms of human NRH-quinone oxidoreductase 2 (NQO2) have different biochemical properties. FEBS Lett. 588, 1666-72

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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: 2.42 Å3/Da / Density % sol: 49.09 % / Description: Yellow Rods
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.7M Ammonium sulfate, 0.1M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 17, 2014
RadiationMonochromator: Osmic Confocol Max-Flux (CMF) graphite monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→15.54 Å / Num. obs: 35891 / % possible obs: 97.9 % / Redundancy: 7 % / Biso Wilson estimate: 21.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Net I/σ(I): 14.3 / Num. measured all: 252057 / Scaling rejects: 141
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.96-2.015.90.6142.81102818800.8970.26773.5
8.99-15.546.40.03434.423073610.9990.01580.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA0.3.6data scaling
PHASER2.5.6phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
MOSFLM7.1.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QR2

1qr2


Resolution: 1.973→15.538 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1765 4.93 %Random selection
Rwork0.1694 34033 --
obs0.1724 35798 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.8 Å2 / Biso mean: 27.859 Å2 / Biso min: 5.87 Å2
Refinement stepCycle: final / Resolution: 1.973→15.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 244 341 4232
Biso mean--37.4 29.24 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123967
X-RAY DIFFRACTIONf_angle_d1.375424
X-RAY DIFFRACTIONf_chiral_restr0.054574
X-RAY DIFFRACTIONf_plane_restr0.007665
X-RAY DIFFRACTIONf_dihedral_angle_d14.0191395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.973-2.02620.2971280.22182501262998
2.0262-2.08570.28951390.203626112750100
2.0857-2.15290.26921320.20325702702100
2.1529-2.22960.31891340.21825872721100
2.2296-2.31860.35231260.26932589271599
2.3186-2.42370.26021340.177325962730100
2.4237-2.5510.23591510.177125982749100
2.551-2.710.22031180.174126332751100
2.71-2.9180.23361270.17526122739100
2.918-3.20930.23171490.167626262775100
3.2093-3.66840.22031530.153426402793100
3.6684-4.60180.16771340.130126752809100
4.6018-15.5380.1861400.13827952935100

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