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- PDB-3fw1: Quinone Reductase 2 -

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Basic information

Entry
Database: PDB / ID: 3fw1
TitleQuinone Reductase 2
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / flavoprotein / metalloprotein / imatinib complex / Cytoplasm / FAD / Metal-binding / Phosphoprotein / Polymorphism / Zinc
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 / oxidoreductase activity / electron transfer activity / protein homodimerization activity / zinc ion binding / extracellular exosome / 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 / Chem-STI / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsWinger, J.A. / Hantschel, O. / Superti-Furga, G. / Kuriyan, J.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2).
Authors: Winger, J.A. / Hantschel, O. / Superti-Furga, G. / Kuriyan, J.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6906
Polymers26,1091
Non-polymers1,5815
Water3,837213
1
A: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules

A: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,37912
Polymers52,2172
Non-polymers3,16210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area10010 Å2
ΔGint-67 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.337, 100.337, 104.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

21A-338-

HOH

31A-373-

HOH

41A-439-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 26108.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct contains two extra N-terminal residues (GA) derived from the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: NMOR2, NQO2 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLysS / References: UniProt: P16083, EC: 1.10.99.2

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Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB


Mass: 493.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31N7O / Comment: medication, inhibitor*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM MES pH 6.0-6.2, 0.015 mM FAD, 62% MPD, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.2547 Å
DetectorType: ADSC QUANTUM Q315r / Detector: AREA DETECTOR / Date: Jul 25, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2547 Å / Relative weight: 1
ReflectionResolution: 1.75→31.864 Å / Num. all: 27269 / Num. obs: 27265 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
1.75-1.849.30.5591.30.559100
1.84-1.969.30.3132.40.313100
1.96-2.099.30.1993.60.199100
2.09-2.269.30.1424.90.142100
2.26-2.479.20.1016.80.101100
2.47-2.779.20.0788.40.078100
2.77-3.29.10.087.40.08100
3.2-3.918.50.0748.20.074100
3.91-5.539.20.04213.20.042100
5.53-36.258.70.03914.40.03999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.38 Å
Translation2.5 Å29.38 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QR2

1qr2


Resolution: 1.75→31.864 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 15.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1817 1395 5.12 %
Rwork0.1499 --
obs0.1515 27265 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.289 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso mean: 30.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å20 Å2
2---0.83 Å2-0 Å2
3---1.407 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 153 257 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123906
X-RAY DIFFRACTIONf_angle_d1.0937052
X-RAY DIFFRACTIONf_dihedral_angle_d21.07973
X-RAY DIFFRACTIONf_chiral_restr0.102288
X-RAY DIFFRACTIONf_plane_restr0.006584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.81260.24861580.21262538X-RAY DIFFRACTION100
1.8126-1.88520.22681340.19672536X-RAY DIFFRACTION100
1.8852-1.97090.20871350.17082552X-RAY DIFFRACTION100
1.9709-2.07480.18751260.15422559X-RAY DIFFRACTION100
2.0748-2.20480.18171500.14182551X-RAY DIFFRACTION100
2.2048-2.3750.18111420.13632569X-RAY DIFFRACTION100
2.375-2.61390.16841300.1312590X-RAY DIFFRACTION100
2.6139-2.99190.17191460.1322576X-RAY DIFFRACTION100
2.9919-3.76850.13861360.12552638X-RAY DIFFRACTION100
3.7685-31.86920.17951380.15292761X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.030.62231.41130.7710.25730.8076-0.28160.26210.1431-0.29220.12160.1853-0.23670.25170.12860.2056-0.0844-0.06390.12530.02810.166827.08625.540511.4777
20.62120.28441.24450.18170.28372.41790.0777-0.13740.0046-0.0513-0.0530.14050.1695-0.3489-0.00230.1247-0.0103-0.04680.1561-0.03860.228710.080711.436425.1805
30.6690.57430.56560.96550.56670.636-0.13450.10340.039-0.18760.13760.1021-0.05840.0955-0.0110.1315-0.0265-0.02040.11380.00210.105126.896415.742315.7479
4-0.09910.7060.64021.51560.3850.08360.04650.2549-0.169-0.06590.3655-0.96310.06090.4326-0.42870.10020.0443-0.00630.2205-0.13850.323951.797916.956324.8825
51.43480.79251.13091.05911.24620.8802-0.19170.5697-0.2849-0.27550.4597-0.3219-0.1750.5241-0.2530.1635-0.09010.04890.3184-0.11360.152541.27315.395412.481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:60)
2X-RAY DIFFRACTION2(chain A and resid 61:78)
3X-RAY DIFFRACTION3(chain A and resid 79:152)
4X-RAY DIFFRACTION4(chain A and resid 153:162)
5X-RAY DIFFRACTION5(chain A and resid 163:229)

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