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- PDB-5ea2: Crystal Structure of Holo NAD(P)H dehydrogenase, quinone 1 -

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Basic information

Entry
Database: PDB / ID: 5ea2
TitleCrystal Structure of Holo NAD(P)H dehydrogenase, quinone 1
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsOXIDOREDUCTASE / NQO1 / two-electron reduction of Quinone / NAD(P)H dehydrogenase
Function / homology
Function and homology information


response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / cytochrome-b5 reductase activity, acting on NAD(P)H ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / cytochrome-b5 reductase activity, acting on NAD(P)H / NADPH oxidation / response to tetrachloromethane / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / response to hydrogen sulfide / response to alkaloid / response to carbohydrate / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to electrical stimulus / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / response to nutrient / cell redox homeostasis / response to hormone / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of neuron apoptotic process / response to estradiol / cellular response to oxidative stress / response to ethanol / response to oxidative stress / response to lipopolysaccharide / innate immune response / neuronal cell body / synapse / dendrite / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
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 / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsPidugu, L.S. / Mbimba, J.E. / Ahmad, M. / Pozharski, E. / Sausville, E.A. / Emadi, A. / Toth, E.A.
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: A direct interaction between NQO1 and a chemotherapeutic dimeric naphthoquinone.
Authors: Pidugu, L.S. / Mbimba, J.C. / Ahmad, M. / Pozharski, E. / Sausville, E.A. / Emadi, A. / Toth, E.A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Data collection / Derived calculations
Category: diffrn_detector / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H dehydrogenase [quinone] 1
C: NAD(P)H dehydrogenase [quinone] 1
E: NAD(P)H dehydrogenase [quinone] 1
G: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,4258
Polymers124,2834
Non-polymers3,1424
Water12,845713
1
A: NAD(P)H dehydrogenase [quinone] 1
C: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7134
Polymers62,1412
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-53 kcal/mol
Surface area22520 Å2
MethodPISA
2
E: NAD(P)H dehydrogenase [quinone] 1
G: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7134
Polymers62,1412
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-54 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.930, 107.160, 99.760
Angle α, β, γ (deg.)90.00, 100.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NAD(P)H dehydrogenase [quinone] 1 / Azoreductase / DT-diaphorase / DTD / Menadione reductase / NAD(P)H:quinone oxidoreductase 1 / ...Azoreductase / DT-diaphorase / DTD / Menadione reductase / NAD(P)H:quinone oxidoreductase 1 / Phylloquinone reductase / Quinone reductase 1 / QR1


Mass: 31070.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO1, DIA4, NMOR1 / Plasmid: 19-PPS
Details (production host): pET19b with a prescission protease cleave site inserted
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350, Ammonium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→45.12 Å / Num. obs: 78225 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 30.05 Å2 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.01-2.057.11.1981.53146544370.6210.48499.7
10.25-45.127.20.0417.844996210.9990.01698.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D4A

1d4a


Resolution: 2.01→44.57 Å / Cor.coef. Fo:Fc: 0.9441 / Cor.coef. Fo:Fc free: 0.9308 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 3933 5.03 %RANDOM
Rwork0.1805 ---
obs0.1823 78180 99.97 %-
Displacement parametersBiso mean: 28.94 Å2
Baniso -1Baniso -2Baniso -3
1-4.4024 Å20 Å22.8663 Å2
2---5.1983 Å20 Å2
3---0.7959 Å2
Refine analyzeLuzzati coordinate error obs: 0.223 Å
Refinement stepCycle: LAST / Resolution: 2.01→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8706 0 212 713 9631
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019176HARMONIC2
X-RAY DIFFRACTIONt_angle_deg112446HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3157SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes202HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1460HARMONIC5
X-RAY DIFFRACTIONt_it9176HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion16.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1150SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11263SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 305 5.29 %
Rwork0.2195 5463 -
all0.2222 5768 -
obs--99.97 %

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