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- PDB-8c9j: Crystal structure of human NQO1 by serial femtosecond crystallography -

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Basic information

Entry
Database: PDB / ID: 8c9j
TitleCrystal structure of human NQO1 by serial femtosecond crystallography
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsOXIDOREDUCTASE / NQO1 / flavoprotein / cancer / serial femtosecond crystallography / microcrystals / XFEL / Droplet injection
Function / homology
Function and homology information


ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / cytochrome-b5 reductase activity, acting on NAD(P)H / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) ...ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / cytochrome-b5 reductase activity, acting on NAD(P)H / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of ferroptosis / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / cell redox homeostasis / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / protein polyubiquitination / cellular response to oxidative stress / response to oxidative stress / response to lipopolysaccharide / innate immune response / synapse / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavoprotein-like superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMartin-Garcia, J.M. / Grieco, A. / Ruiz-Fresneda, M.A. / Pacheco-Garcia, J.L. / Pey, A. / Botha, S. / Ros, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Comunidad de Madrid2019-T1BMD-15552 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-096246-B-I00 Spain
CitationJournal: Lab Chip / Year: 2023
Title: Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme.
Authors: Doppler, D. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. / Alvarez, R.C. / Karpos, K. / Cruz Villarreal, J. / ...Authors: Doppler, D. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. / Alvarez, R.C. / Karpos, K. / Cruz Villarreal, J. / Nelson, G. / Yang, J.H. / Carrion, J. / Morin, K. / Ketawala, G.K. / Pey, A.L. / Ruiz-Fresneda, M.A. / Pacheco-Garcia, J.L. / Hermoso, J.A. / Nazari, R. / Sierra, R. / Hunter, M.S. / Batyuk, A. / Kupitz, C.J. / Sublett, R.E. / Lisova, S. / Mariani, V. / Boutet, S. / Fromme, R. / Grant, T.D. / Botha, S. / Fromme, P. / Kirian, R.A. / Martin-Garcia, J.M. / Ros, A.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,00912
Polymers123,6304
Non-polymers3,3788
Water2,936163
1
A: NAD(P)H dehydrogenase [quinone] 1
B: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4455
Polymers61,8152
Non-polymers1,6303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-53 kcal/mol
Surface area22030 Å2
MethodPISA
2
C: NAD(P)H dehydrogenase [quinone] 1
D: NAD(P)H dehydrogenase [quinone] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5637
Polymers61,8152
Non-polymers1,7485
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-54 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.400, 107.600, 198.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 272
2111A3 - 272
3221A3 - 272
4221A3 - 272
5331A3 - 273
6331A3 - 273
7441A2 - 273
8441A2 - 273
9551A3 - 272
10551A3 - 272
11661A3 - 272
12661A3 - 272

NCS ensembles :
IDDetails
1Global NCS restraints between domains: 1 2
2Global NCS restraints between domains: 3 4
3Global NCS restraints between domains: 5 6
4Global NCS restraints between domains: 7 8
5Global NCS restraints between domains: 9 10
6Global NCS restraints between domains: 11 12

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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: 30907.611 Da / Num. of mol.: 4 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO1, DIA4, NMOR1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.52 % / Description: Needles
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350, 20 um FAD

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.2848 Å
DetectorType: SLAC ePix10k / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2848 Å / Relative weight: 1
ReflectionResolution: 2.7→24 Å / Num. obs: 36928 / % possible obs: 100 % / Redundancy: 46 % / CC1/2: 0.9668 / CC star: 0.9234 / Net I/σ(I): 1.9
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 3619 / CC1/2: 0.458 / CC star: 0.5202 / % possible all: 100
Serial crystallography sample deliveryDescription: Modular Droplet Injector / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: Crystals in mother liquor encapsulated into oil droplets
Crystal conc.: 1000 / Description: Modular Droplet Injector / Flow rate: 5 µL/min / Injector temperature: 298 K
Serial crystallography data reductionXFEL pulse events: 40

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
CrystFELdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DXQ

1dxq


Resolution: 2.7→23.922 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.878 / SU B: 28.385 / SU ML: 0.508 / Cross valid method: FREE R-VALUE / ESU R Free: 0.377
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1822 4.946 %0.1
Rwork0.225 35013 --
all0.227 ---
obs-36835 99.724 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.992 Å2
Baniso -1Baniso -2Baniso -3
1-0.363 Å20 Å20 Å2
2--0.054 Å20 Å2
3----0.417 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8646 0 228 163 9037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129213
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168643
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.64312500
X-RAY DIFFRACTIONr_angle_other_deg0.3811.57319944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69851096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.131537
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.32454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.632101548
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.85910403
X-RAY DIFFRACTIONr_chiral_restr0.050.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210489
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022143
X-RAY DIFFRACTIONr_nbd_refined0.2110.21547
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.27489
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24418
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2152
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2790.211
X-RAY DIFFRACTIONr_nbd_other0.2740.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.23
X-RAY DIFFRACTIONr_mcbond_it2.4914.5114379
X-RAY DIFFRACTIONr_mcbond_other2.494.5094377
X-RAY DIFFRACTIONr_mcangle_it4.1728.1015474
X-RAY DIFFRACTIONr_mcangle_other4.1728.1025475
X-RAY DIFFRACTIONr_scbond_it2.7144.8624834
X-RAY DIFFRACTIONr_scbond_other2.7144.8634835
X-RAY DIFFRACTIONr_scangle_it4.6998.7657026
X-RAY DIFFRACTIONr_scangle_other4.6998.7657027
X-RAY DIFFRACTIONr_lrange_it7.23244.92110345
X-RAY DIFFRACTIONr_lrange_other7.23244.92410346
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight Biso : 0.866 / Weight position: 0.0866

Ens-IDDom-IDRms dev Biso (Å2)Rms dev position (Å)
113.833540.19954
123.833540.19954
236.81010.18503
246.81010.18503
358.225750.20487
368.225750.20487
476.768870.26021
486.768870.26021
597.817760.19006
5107.817760.19006
6116.436910.19857
6126.436910.19857
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.7-2.7690.3961290.38425280.38526590.660.68399.92480.393
2.769-2.8440.3591230.36124540.36125790.8820.88599.92240.369
2.844-2.9250.3661200.35624080.35625320.8860.89199.8420.364
2.925-3.0140.3531410.3522880.3524300.880.90299.95880.357
3.014-3.1110.3041220.32522550.32423800.9260.90999.87390.335
3.111-3.2180.3041090.28121930.28223030.9350.93999.95660.288
3.218-3.3380.2821280.25921050.26122330.940.9491000.266
3.338-3.4710.3141110.25220510.25521630.9270.95299.95380.259
3.471-3.6220.2651080.21319660.21620750.9480.96899.95180.22
3.622-3.7940.2341030.19518620.19719650.9630.9731000.201
3.794-3.9940.2771000.19118020.19619030.950.97399.94740.199
3.994-4.2290.263860.17917050.18317910.9520.9771000.189
4.229-4.5110.189900.1516240.15217140.9740.9841000.156
4.511-4.8580.195730.15615090.15815820.9760.9831000.162
4.858-5.30.192570.14614210.14814780.9740.9851000.155
5.3-5.8890.248480.16813030.1713510.9570.9811000.175
5.889-6.7330.256590.17111620.17412210.960.9791000.178
6.733-8.0870.218440.17510060.17710500.9750.9781000.186
8.087-10.8350.215450.1498200.1538650.9690.9841000.164
10.835-23.9220.305260.3215510.3215880.9510.9498.12930.46

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