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Basic information

Entry
Database: PDB / ID: 3nhr
TitleX-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and its Analogs Bound to Human Quinone Reductase 2
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / protein dimer / 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 / 5,6,8-trimethoxy-1,4-dimethylquinolin-2(1H)-one / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSturdy, M.
Citation
Journal: To be Published
Title: X-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and its Analogs Bound to Human Quinone Reductase 2
Authors: Sturdy, M.
#1: Journal: J.Med.Chem. / Year: 2009
Title: Synthesis of casimiroin and optimization of its quinone reductase 2 and aromatase inhibitory activities.
Authors: Maiti, A. / Reddy, P.V. / Sturdy, M. / Marler, L. / Pegan, S.D. / Mesecar, A.D. / Pezzuto, J.M. / Cushman, M.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2May 31, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_auth_seq_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_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)54,1909
Polymers51,6992
Non-polymers2,4927
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-33 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.781, 83.610, 106.632
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: pET-23d / 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-RZW / 5,6,8-trimethoxy-1,4-dimethylquinolin-2(1H)-one


Mass: 263.289 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H17NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.7
Details: 1.339 M ammonium sulfate, 0.1 M Bis-Tris, 0.1 M NaCl, 5 mM DTT, 12 uM FAD, pH 6.7, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 27.52 / Number: 231772 / Rmerge(I) obs: 0.058 / Χ2: 1.09 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 47287 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.885099.210.020.7934.6
3.884.8899.510.0220.8444.8
3.393.8899.510.0311.1414.9
3.083.3999.510.041.2474.9
2.863.0899.310.0521.4695
2.692.8699.410.0581.2945
2.552.6999.110.0671.2035
2.442.559910.0640.9025
2.352.4498.710.0680.8865
2.272.3599.110.0790.9235
2.22.2798.510.1071.2244.9
2.132.29910.1080.9735
2.082.1398.310.131.0755
2.032.0898.110.1751.4584.9
1.982.0398.510.1560.9424.9
1.941.9898.210.1961.0684.9
1.91.9497.910.2731.3414.8
1.861.997.810.2991.134.9
1.831.8697.510.2850.8894.9
1.81.8397.310.3050.9034.8
ReflectionResolution: 1.8→65.8 Å / Num. obs: 47287 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.058 / Χ2: 1.086 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.834.80.30523160.903197.3
1.83-1.864.90.28522780.889197.5
1.86-1.94.90.29923151.13197.8
1.9-1.944.80.27323201.341197.9
1.94-1.984.90.19623301.068198.2
1.98-2.034.90.15623130.942198.5
2.03-2.084.90.17523081.458198.1
2.08-2.1350.1323401.075198.3
2.13-2.250.10823650.973199
2.2-2.274.90.10723331.224198.5
2.27-2.3550.07923400.923199.1
2.35-2.4450.06823420.886198.7
2.44-2.5550.06423650.902199
2.55-2.6950.06723791.203199.1
2.69-2.8650.05823731.294199.4
2.86-3.0850.05223951.469199.3
3.08-3.394.90.0424071.247199.5
3.39-3.884.90.03124291.141199.5
3.88-4.884.80.02224530.844199.5
4.88-504.60.0225860.793199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2046 / WRfactor Rwork: 0.1686 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8464 / SU B: 2.644 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1275 / SU Rfree: 0.1214 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 2394 5.1 %RANDOM
Rwork0.1788 ---
obs0.1806 47242 98.55 %-
all-47287 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.07 Å2 / Biso mean: 19.4856 Å2 / Biso min: 3.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--0.37 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 165 378 4186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223949
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.9995390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69524.22173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03615614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2871516
X-RAY DIFFRACTIONr_chiral_restr0.1680.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213006
X-RAY DIFFRACTIONr_mcbond_it1.4361.52287
X-RAY DIFFRACTIONr_mcangle_it2.29923686
X-RAY DIFFRACTIONr_scbond_it3.26331662
X-RAY DIFFRACTIONr_scangle_it4.9094.51704
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 170 -
Rwork0.263 3149 -
all-3319 -
obs--95.13 %

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