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Basic information

Entry
Database: PDB / ID: 3nhj
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
6,9-dimethyl[1,3]dioxolo[4,5-h]quinolin-8(9H)-one / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)53,8358
Polymers51,6992
Non-polymers2,1366
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-33 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.126, 83.594, 106.367
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-A2Z / 6,9-dimethyl[1,3]dioxolo[4,5-h]quinolin-8(9H)-one


Mass: 217.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
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, and 12 uM FAD, pH 6.7, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 298 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: 5 % / Av σ(I) over netI: 23.08 / Number: 105232 / Rmerge(I) obs: 0.097 / Χ2: 1.93 / D res high: 2.33 Å / D res low: 50 Å / Num. obs: 21122 / % possible obs: 95.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.025089.710.0583.434.8
3.985.0294.210.0653.5934.9
3.483.9894.610.0843.4274.8
3.163.4895.410.0952.0755.1
2.943.1696.310.1191.545
2.762.9496.210.1741.3695.1
2.622.7696.910.2291.1315
2.512.6296.910.2920.975.1
2.412.5197.510.3391.0015
2.332.4197.810.4281.0025
ReflectionResolution: 2.33→65.8 Å / Num. obs: 21122 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.097 / Χ2: 1.932 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.33-2.4150.42821141.002197.8
2.41-2.5150.33921161.001197.5
2.51-2.625.10.29221100.97196.9
2.62-2.7650.22921091.131196.9
2.76-2.945.10.17421031.369196.2
2.94-3.1650.11921081.54196.3
3.16-3.485.10.09521142.075195.4
3.48-3.984.80.08421023.427194.6
3.98-5.024.90.06521163.593194.2
5.02-504.80.05821303.43189.7

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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: 2.33→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2538 / WRfactor Rwork: 0.1904 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8037 / SU B: 7.4 / SU ML: 0.184 / SU R Cruickshank DPI: 0.4483 / SU Rfree: 0.2841 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 1082 5.1 %RANDOM
Rwork0.1968 ---
obs0.2003 21081 95.51 %-
all-1458 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.29 Å2 / Biso mean: 38.6836 Å2 / Biso min: 9.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2--0.24 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 140 116 3904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223906
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9875329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85724.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81715615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5311516
X-RAY DIFFRACTIONr_chiral_restr0.120.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212968
X-RAY DIFFRACTIONr_mcbond_it1.0341.52289
X-RAY DIFFRACTIONr_mcangle_it1.89723688
X-RAY DIFFRACTIONr_scbond_it2.56331617
X-RAY DIFFRACTIONr_scangle_it3.9164.51640
LS refinement shellResolution: 2.33→2.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 93 -
Rwork0.22 1458 -
all-1551 -
obs--97.49 %

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