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

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Basic information

Entry
Database: PDB / ID: 3nhp
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 / 6,7,8-trimethoxy-4-methylquinolin-2(1H)-one / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)53,8998
Polymers51,6992
Non-polymers2,2006
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-32 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.426, 83.479, 106.461
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-HGZ / 6,7,8-trimethoxy-4-methylquinolin-2(1H)-one


Mass: 249.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.42 Å3/Da / Density % sol: 49.28 %
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: 4.7 % / Av σ(I) over netI: 25.53 / Number: 228285 / Rmerge(I) obs: 0.054 / Χ2: 1.05 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 48856 / % possible obs: 86.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.615094.210.0291.574.6
3.664.6158.310.0271.4154.2
3.23.6672.510.0351.54.3
2.913.299.910.0480.5564.9
2.72.9110010.0560.674.9
2.542.710010.0591.7554.9
2.412.5410010.0621.5124.9
2.312.4110010.0651.2585
2.222.3129.410.0972.012.4
2.142.2280.110.0841.0124.8
2.072.1499.910.0790.8274.9
2.022.0799.910.0910.7755
1.962.0299.910.1240.8525
1.911.9665.910.1572.0153.5
1.871.9136.110.2081.3233.6
1.831.8799.910.2290.8184.9
1.791.8399.910.2220.7744.9
1.761.7999.910.2560.7694.9
1.731.7698.810.2430.7474.6
1.71.7397.910.2480.7244.3
ReflectionResolution: 1.7→65.69 Å / Num. obs: 48856 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.054 / Χ2: 1.049 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.734.30.24827060.724197.9
1.73-1.764.60.24327770.747198.8
1.76-1.794.90.25627580.769199.9
1.79-1.834.90.22227920.774199.9
1.83-1.874.90.22927870.818199.9
1.87-1.913.60.2089951.323136.1
1.91-1.963.50.15718522.015165.9
1.96-2.0250.12427750.852199.9
2.02-2.0750.09127920.775199.9
2.07-2.144.90.07927780.827199.9
2.14-2.224.80.08422521.012180.1
2.22-2.312.40.0978212.01129.4
2.31-2.4150.06528181.2581100
2.41-2.544.90.06228101.5121100
2.54-2.74.90.05928261.7551100
2.7-2.914.90.05628170.671100
2.91-3.24.90.04828530.556199.9
3.2-3.664.30.03520771.5172.5
3.66-4.614.20.02716951.415158.3
4.61-504.60.02928751.57194.2

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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: 1.7→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2623 / WRfactor Rwork: 0.2065 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7974 / SU B: 2.526 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1452 / SU Rfree: 0.1438 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 2457 5.1 %RANDOM
Rwork0.2129 ---
obs0.2155 48642 86.13 %-
all-48856 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.52 Å2 / Biso mean: 23.4964 Å2 / Biso min: 5.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--0.26 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 144 379 4171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223902
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.9875320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79324.186172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35715612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0061516
X-RAY DIFFRACTIONr_chiral_restr0.1430.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212964
X-RAY DIFFRACTIONr_mcbond_it1.3421.52286
X-RAY DIFFRACTIONr_mcangle_it2.13323682
X-RAY DIFFRACTIONr_scbond_it3.0531616
X-RAY DIFFRACTIONr_scangle_it4.6274.51638
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 193 -
Rwork0.251 3692 -
all-3885 -
obs--94.5 %

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