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- PDB-4u7h: Oxidized quinone reductase 2 in complex with CK2 inhibitor DMAT -

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Basic information

Entry
Database: PDB / ID: 4u7h
TitleOxidized quinone reductase 2 in complex with CK2 inhibitor DMAT
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOxidoreductase/Inhibitor / reduced quinone reductase 2 / DMAT / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 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 1.1Nov 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 1.2Dec 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
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-31 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.250, 83.010, 106.480
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 48.84 %
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: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 19, 2011 / Details: 16 CCDs, 16 tiled fiber-optic tapers
RadiationMonochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→30.017 Å / Num. obs: 85781 / % possible obs: 96 % / Redundancy: 4.6 % / Biso Wilson estimate: 15.64 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.08 / Rsym value: 0.063 / Net I/av σ(I): 7.996 / Net I/σ(I): 9.7 / Num. measured all: 395937
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.45-1.533.10.4281.72941696020.320.4281.774.5
1.53-1.624.60.374255517121980.2210.3742.9100
1.62-1.734.80.2842.655532115380.160.2843.9100
1.73-1.874.80.1784.251863107390.1010.1785.6100
1.87-2.054.90.1126.44810698980.0630.1128.6100
2.05-2.294.90.10464380489730.0560.10412.299.9
2.29-2.644.90.0679.63890079420.0360.06715.799.8
2.64-3.244.90.05111.73313667300.0280.05120.499.3
3.24-4.584.90.03417.52571652200.0190.03427.798.4
4.58-30.0174.70.03217.91394729410.0180.03226.396.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→30.017 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 2072 2.49 %
Rwork0.179 81247 -
obs0.1797 83319 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.86 Å2 / Biso mean: 24.3113 Å2 / Biso min: 9.09 Å2
Refinement stepCycle: final / Resolution: 1.48→30.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 172 551 4370
Biso mean--27.52 31.79 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013966
X-RAY DIFFRACTIONf_angle_d1.3855421
X-RAY DIFFRACTIONf_chiral_restr0.073564
X-RAY DIFFRACTIONf_plane_restr0.007672
X-RAY DIFFRACTIONf_dihedral_angle_d14.8021399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.51440.31971260.302753215447100
1.5144-1.55230.3081360.262253905526100
1.5523-1.59430.27061410.240953615502100
1.5943-1.64120.24971370.227553925529100
1.6412-1.69420.27261360.222953915527100
1.6942-1.75470.22341290.209454055534100
1.7547-1.82490.26891410.203454015542100
1.8249-1.9080.23451390.201353735512100
1.908-2.00860.21571370.189854485585100
2.0086-2.13440.24741370.184354105547100
2.1344-2.29910.21721390.17954235562100
2.2991-2.53040.21351400.169654565596100
2.5304-2.89630.20371420.17815439558199
2.8963-3.6480.16011480.15785472562099
3.648-30.02330.16791440.14475565570997

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