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- PDB-4fgj: Oxidized quinone reductase 2 in complex with primaquine -

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Basic information

Entry
Database: PDB / ID: 4fgj
TitleOxidized quinone reductase 2 in complex with primaquine
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
Keywordsoxidoreductase/oxidoreductase inhibitor / primaquine / FMN reductase superfamily / 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-1PQ / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.346 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 1.1Feb 28, 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_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_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_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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,62210
Polymers52,2172
Non-polymers2,4058
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-29 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 83.000, 106.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 26108.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Coding region of NQO2 was inserted into vector pProEXhta (Invitrogen)
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

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Non-polymers , 5 types, 566 molecules

#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-1PQ / (4S)-N~4~-(6-methoxyquinolin-8-yl)pentane-1,4-diamine / primaquine


Mass: 259.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N3O / Comment: medication*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.55 %
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: 08B1-1 / Wavelength: 1.033217 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 18, 2011 / Details: 16 CCDs, 16 tiled fiber-optic tapers
RadiationMonochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033217 Å / Relative weight: 1
ReflectionResolution: 1.346→30.057 Å / Num. all: 110793 / Num. obs: 110793 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 12.124 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.424.80.631.276359158960.6398.8
1.42-1.54.80.4131.872547150700.41399.1
1.5-1.614.80.2622.968536142370.26299.4
1.61-1.744.80.1873.964332133100.18799.6
1.74-1.94.90.1146.360041123210.11499.8
1.9-2.134.90.0857.755040112150.085100
2.13-2.464.90.0748.34891199500.074100
2.46-3.014.90.05211.74138884310.052100
3.01-4.264.90.03416.93232766280.034100
4.26-30.0574.70.03119.11748937350.03198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å30.06 Å
Translation2.5 Å30.06 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.4.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.346→30.057 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 15.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1666 1999 1.81 %
Rwork0.1413 108709 -
obs0.1417 110708 99.37 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.31 Å2 / Biso mean: 14.6476 Å2 / Biso min: 1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.346→30.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 158 558 4364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084001
X-RAY DIFFRACTIONf_angle_d1.2555451
X-RAY DIFFRACTIONf_chiral_restr0.07573
X-RAY DIFFRACTIONf_plane_restr0.006672
X-RAY DIFFRACTIONf_dihedral_angle_d14.5941399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.346-1.37970.28031390.23667620775998
1.3797-1.4170.24071400.20937608774899
1.417-1.45870.22451400.19237623776399
1.4587-1.50570.2031420.17747672781499
1.5057-1.55950.19791410.14817665780699
1.5595-1.6220.18951420.13287717785999
1.622-1.69580.15811410.13047711785299
1.6958-1.78520.17091430.123877447887100
1.7852-1.8970.16191430.118577867929100
1.897-2.04350.15911440.115577897933100
2.0435-2.2490.14741440.118578527996100
2.249-2.57430.14371450.123978477992100
2.5743-3.24280.16061460.145579318077100
3.2428-30.06450.15631490.14938144829399

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