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- PDB-4u7f: Reduced quinone reductase 2 in complex with CK2 inhibitor DMAT -

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Basic information

Entry
Database: PDB / ID: 4u7f
TitleReduced quinone reductase 2 in complex with CK2 inhibitor DMAT
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOxidoreductase/Inhibitor / reduced quinone reductase 2 / DMAT / CK2 inhibitor / 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-K25 / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
Model detailsMetallo-flavoprotein
AuthorsLeung, K.K. / Shilton, B.H.
CitationJournal: Biochemistry / Year: 2015
Title: Quinone Reductase 2 Is an Adventitious Target of Protein Kinase CK2 Inhibitors TBBz (TBI) and DMAT.
Authors: Leung, K.K. / Shilton, B.H.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: 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)54,3548
Polymers51,6992
Non-polymers2,6556
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-30 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.120, 83.140, 106.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer and has two active sites. The inhibitor binds NQO2 in two orientations in both active sites.

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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-K25 / 4,5,6,7-TETRABROMO-N,N-DIMETHYL-1H-BENZIMIDAZOL-2-AMINE / DIMETHYL-(4,5,6,7-TETRABROMO-1H-BENZOIMIDAZOL-2-YL)-AMINE


Mass: 476.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7Br4N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging 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 RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 2, 2011
RadiationMonochromator: Osmic Confocol Max-Flux (CMF) graphite monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→17.988 Å / Num. all: 47314 / Num. obs: 47314 / % possible obs: 89.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.59 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Rsym value: 0.073 / Net I/av σ(I): 9.074 / Net I/σ(I): 14.8 / Num. measured all: 295666
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.73-1.8260.6581.23358356400.2980.6582.674.5
1.82-1.936.20.4591.73807261350.2050.4593.985.4
1.93-2.0760.2632.93543158850.1180.263687.5
2.07-2.235.80.1684.53321557410.0780.1688.791.2
2.23-2.445.80.1166.53234555410.0550.11611.894.8
2.44-2.736.40.098.43222950590.0420.0915.396
2.73-3.156.80.06211.83108745590.0280.0622296.8
3.15-3.866.90.044152713139130.0190.04434.697.6
3.86-5.466.90.03120.62125430850.0140.03142.298.2
5.46-17.9886.40.0316.21131917560.0140.0337.996

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
MOSFLMdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→17.935 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1762 4.23 %random selection
Rwork0.1863 75727 --
obs0.1879 43375 88.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.87 Å2 / Biso mean: 24.8811 Å2 / Biso min: 7.98 Å2
Refinement stepCycle: final / Resolution: 1.8→17.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 172 228 4048
Biso mean--24.95 26.76 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083950
X-RAY DIFFRACTIONf_angle_d1.1575396
X-RAY DIFFRACTIONf_chiral_restr0.044562
X-RAY DIFFRACTIONf_plane_restr0.006670
X-RAY DIFFRACTIONf_dihedral_angle_d14.1021396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82570.32331260.27272776290278
1.8257-1.85290.31141250.28112776290178
1.8529-1.88180.33061230.25912823294679
1.8818-1.91270.32551260.2492810293679
1.9127-1.94560.31261270.22262836296380
1.9456-1.98090.26741320.21552905303782
1.9809-2.0190.24811300.20812892302281
2.019-2.06010.24571320.19522942307483
2.0601-2.10490.21061300.19182943307383
2.1049-2.15380.20841340.19263059319385
2.1538-2.20750.23681340.19223086322088
2.2075-2.26710.25191430.18633129327288
2.2671-2.33370.23421420.18153248339091
2.3337-2.40880.24431470.1823302344992
2.4088-2.49470.25451420.18793293343593
2.4947-2.59430.25011480.18693366351495
2.5943-2.7120.20271490.19093397354696
2.712-2.85440.21151520.1983390354296
2.8544-3.03250.24991450.2023450359596
3.0325-3.26530.24871550.18923429358497
3.2653-3.59160.17921490.1763452360197
3.5916-4.10580.18671540.15793461361597
4.1058-5.15250.19111530.14683491364498
5.1525-17.93590.18231470.1783471361898

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