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- PDB-3nhl: X-ray Crystallographic Structure Activity Relationship (SAR) of C... -

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Basic information

Entry
Database: PDB / ID: 3nhl
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 / 7,8-dimethoxy-1,4-dimethylquinolin-2(1H)-one / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)53,8678
Polymers51,6992
Non-polymers2,1686
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-32 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.104, 83.163, 106.473
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-YTR / 7,8-dimethoxy-1,4-dimethylquinolin-2(1H)-one


Mass: 233.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 48.8 %
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: 4.8 % / Av σ(I) over netI: 35.95 / Number: 326557 / Rmerge(I) obs: 0.047 / Χ2: 1.36 / D res high: 1.57 Å / D res low: 50 Å / Num. obs: 67732 / % possible obs: 96.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.265081.710.0271.6654.9
3.384.269210.031.6815
2.953.3894.910.0452.4575.1
2.682.9595.910.0572.8135
2.492.6896.210.0592.3335.1
2.352.4997.110.0561.8245.1
2.232.3597.610.0571.5855.1
2.132.239810.0581.2135.1
2.052.139810.0631.1065
1.982.0598.510.0711.0465
1.921.9898.310.0891.0684.9
1.861.9298.910.1081.0284.9
1.811.8699.110.1260.9484.9
1.771.8199.110.1410.9044.8
1.731.7799.110.1620.8944.8
1.691.7399.410.1930.8594.7
1.661.6999.510.230.8544.6
1.631.669910.240.8454.4
1.61.6397.510.2560.8574.1
1.571.693.810.270.7923.9
ReflectionResolution: 1.57→65.54 Å / Num. obs: 67732 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.047 / Χ2: 1.363 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.57-1.63.90.2732440.792193.8
1.6-1.634.10.25633690.857197.5
1.63-1.664.40.2434300.845199
1.66-1.694.60.2334340.854199.5
1.69-1.734.70.19334320.859199.4
1.73-1.774.80.16234470.894199.1
1.77-1.814.80.14134460.904199.1
1.81-1.864.90.12634320.948199.1
1.86-1.924.90.10834061.028198.9
1.92-1.984.90.08934461.068198.3
1.98-2.0550.07134131.046198.5
2.05-2.1350.06334351.106198
2.13-2.235.10.05834241.213198
2.23-2.355.10.05734081.585197.6
2.35-2.495.10.05634111.824197.1
2.49-2.685.10.05933842.333196.2
2.68-2.9550.05734012.813195.9
2.95-3.385.10.04533612.457194.9
3.38-4.2650.0333201.681192
4.26-504.90.02730891.665181.7

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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: 1.57→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2331 / WRfactor Rwork: 0.1959 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8484 / SU B: 1.572 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0915 / SU Rfree: 0.0952 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3424 5.1 %RANDOM
Rwork0.1909 ---
obs0.1929 67677 96.63 %-
all-67732 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.32 Å2 / Biso mean: 25.6854 Å2 / Biso min: 8.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2---0.05 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 142 384 4174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223900
X-RAY DIFFRACTIONr_angle_refined_deg2.4361.9865318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47324.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80415612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5191516
X-RAY DIFFRACTIONr_chiral_restr0.1670.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212964
X-RAY DIFFRACTIONr_mcbond_it1.5781.52286
X-RAY DIFFRACTIONr_mcangle_it2.48523682
X-RAY DIFFRACTIONr_scbond_it3.33331614
X-RAY DIFFRACTIONr_scangle_it4.9684.51636
LS refinement shellResolution: 1.57→1.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 255 -
Rwork0.247 4590 -
all-4845 -
obs--94.96 %

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