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- PDB-4fgl: Reduced quinone reductase 2 in complex with chloroquine -

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Basic information

Entry
Database: PDB / ID: 4fgl
TitleReduced quinone reductase 2 in complex with chloroquine
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / chloroquine / FMN reductase superfamily (conserved domain database) / metallo-flavoprotein / Rossmann fold / two-electron reduction of quinones to hydroquinones / FAD binding / Zn binding / cytosol / 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
Chem-CLQ / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsLeung, K.K. / Shilton, B.H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal structures of quinone reductase 2 bound to antimalarial drugs reveal conformational change upon reduction
Authors: Leung, K.K. / Shilton, B.H.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_label_asym_id / _struct_ref_seq_dif.details / _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]
C: Ribosyldihydronicotinamide dehydrogenase [quinone]
D: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,43817
Polymers104,4354
Non-polymers5,00313
Water19,3121072
1
A: Ribosyldihydronicotinamide dehydrogenase [quinone]
B: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5598
Polymers52,2172
Non-polymers2,3426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-47 kcal/mol
Surface area17940 Å2
MethodPISA
2
C: Ribosyldihydronicotinamide dehydrogenase [quinone]
D: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8799
Polymers52,2172
Non-polymers2,6627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-47 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.310, 105.710, 82.000
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosyldihydronicotinamide dehydrogenase [quinone] / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone reductase 2 / QR2


Mass: 26108.666 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMOR2, NQO2 / Plasmid: pProNQO2 / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-CLQ / N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE / CHLOROQUINE / Chloroquine


Mass: 319.872 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H26ClN3 / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1072 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THE CONFLICT BETWEEN RESIDUE F46 IN THE COORDINATES AND L47, FROM THE ...AUTHORS HAVE INDICATED THAT THE CONFLICT BETWEEN RESIDUE F46 IN THE COORDINATES AND L47, FROM THE UNP P16083, ARISES FROM AN INCORRECT ANNOTATION IN THE UNP ENTRY

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7M Ammonium sulfate, 0.1M Hepes , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 1, 2012 / Details: 9CCD, 9 tiled fiber-optic tapers
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.2→48.307 Å / Num. all: 287744 / Num. obs: 287298 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 13.543 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.048 / Net I/σ(I): 19.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsRsym value% possible all
1.2-1.233.590.2884.367626421233212330.33999.9
1.23-1.263.610.2425.117473420689206890.28599.9
1.26-1.33.640.2065.927300820072200720.24399.9
1.3-1.343.660.1826.817133619509195090.21399.9
1.34-1.393.670.1577.846974318978189780.18499.9
1.39-1.433.680.1359.116750118318183180.15899.9
1.43-1.493.710.10811.326562917707177070.12699.9
1.49-1.553.720.08614.046328117002170020.10199.9
1.55-1.623.730.07216.966081616304163040.08499.9
1.62-1.73.740.06119.855852315656156560.07199.9
1.7-1.793.740.05123.45526814790147900.0699.7
1.79-1.93.730.04227.375242914048140480.0599.8
1.9-2.033.720.03533.044918613216132160.04199.8
2.03-2.193.70.0337.514547212281122810.03599.8
2.19-2.43.70.02840.74191411323113230.03399.7
2.4-2.683.710.02742.573786810203102030.03199.8
2.68-3.13.70.02545.1533541905490540.02999.8
3.1-3.793.710.02348.5528411766276620.02799.7
3.79-5.373.720.02150.1122128595359530.02599.9
5.37-48.3073.680.02449.5512137330033000.02899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.4 Å48.31 Å
Translation1.4 Å48.31 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.4.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QR2

1qr2


Resolution: 1.2→48.307 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.9283 / SU ML: 0.1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1735 14365 5 %RANDOM, 5%
Rwork0.1588 ---
obs0.1596 287298 99.84 %-
all-287744 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.195 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 66.45 Å2 / Biso mean: 12.8001 Å2 / Biso min: 3.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.4307 Å2-0 Å20.1275 Å2
2---1.1656 Å20 Å2
3----0.2651 Å2
Refinement stepCycle: LAST / Resolution: 1.2→48.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7313 0 326 1072 8711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097920
X-RAY DIFFRACTIONf_angle_d1.31110796
X-RAY DIFFRACTIONf_chiral_restr0.0721142
X-RAY DIFFRACTIONf_plane_restr0.0071338
X-RAY DIFFRACTIONf_dihedral_angle_d13.9882802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
1.1999-1.21360.19594790.2054910095799100
1.2136-1.22780.20564760.1997904995259049
1.2278-1.24280.20674760.193903995159039
1.2428-1.25850.20424790.1902911295919112
1.2585-1.27510.20384770.1869905995369059
1.2751-1.29260.20364790.1839909695759096
1.2926-1.3110.19424750.1805903895139038
1.311-1.33060.1864800.1743910995899109
1.3306-1.35140.19194780.1726908995679089
1.3514-1.37360.20284760.1726903895149038
1.3736-1.39720.19454790.1674910595849105
1.3972-1.42270.19554790.1657910395829103
1.4227-1.450.18164780.1586908495629084
1.45-1.47960.18074770.156905095279050
1.4796-1.51180.16664820.1516916296449162
1.5118-1.5470.16554770.1449907295499072
1.547-1.58570.16224790.1464910195809101
1.5857-1.62850.15044780.1463907595539075
1.6285-1.67640.17194790.1457911095899110
1.6764-1.73060.16234770.1448906195389061
1.7306-1.79240.16734790.1443909695759096
1.7924-1.86420.1624790.1465910995889109
1.8642-1.9490.16284800.1475911795979117
1.949-2.05180.1544790.1485909295719092
2.0518-2.18030.16694790.1487909795769097
2.1803-2.34870.16134800.1442912696069126
2.3487-2.5850.15924790.1491910495839104
2.585-2.9590.184800.1633912096009120
2.959-3.72790.17834810.1607914396249143
3.7279-48.34650.1694890.1664927797669277

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