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- PDB-8rfn: Human NOQ1 enzyme in its holo form by serial crystallography -

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Basic information

Entry
Database: PDB / ID: 8rfn
TitleHuman NOQ1 enzyme in its holo form by serial crystallography
ComponentsNAD(P)H dehydrogenase [quinone] 1
KeywordsFLAVOPROTEIN / Human NQO1 / oxidoreductase / flavoenzyme
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 / response to oxidative stress / cellular response to oxidative stress / response to lipopolysaccharide / innate immune response / synapse / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMartin-Garcia, J.M. / Grieco, A. / Medina, M. / Boneta, S. / Pey, A.L.
Funding support Spain, 2items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)CNS2022-135713 Spain
Comunidad de Madrid2019-T1/BMD-15552 Spain
Citation
Journal: Protein Sci. / Year: 2024
Title: Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations.
Authors: Grieco, A. / Boneta, S. / Gavira, J.A. / Pey, A.L. / Basu, S. / Orlans, J. / Sanctis, D. / Medina, M. / Martin-Garcia, J.M.
#1: Journal: Protein Sci / Year: 2024
Title: Human NOQ1 enzyme in its holo form by serial crystallography
Authors: Martin-Garcia, J.M. / Grieco, A. / Medina, M. / Boneta, S. / Pey, A.L.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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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
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)127,0119
Polymers123,6304
Non-polymers3,3815
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.000, 108.000, 200.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO1, DIA4, NMOR1 / Production host: Escherichia coli BL21 (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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
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

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Feb 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 41455 / % possible obs: 97.1 % / Redundancy: 154.1 % / CC star: 0.989 / R split: 0.142 / Net I/σ(I): 9.9
Reflection shellResolution: 2.5→2.56 Å / Num. unique obs: 41455 / CC star: 0.532 / R split: 1.5
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Small SOS chips

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.936 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 0.666 / ESU R Free: 0.291
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23869 4581 10 %RANDOM
Rwork0.19873 ---
obs0.20281 41455 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.291 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.08 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8882 0 15 75 8972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129177
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168637
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.6612445
X-RAY DIFFRACTIONr_angle_other_deg0.4621.58419934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52251089
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.995536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84101548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.21313
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022121
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4826.8924362
X-RAY DIFFRACTIONr_mcbond_other5.4816.8924362
X-RAY DIFFRACTIONr_mcangle_it8.42812.435449
X-RAY DIFFRACTIONr_mcangle_other8.42712.4315450
X-RAY DIFFRACTIONr_scbond_it4.957.1454815
X-RAY DIFFRACTIONr_scbond_other4.9367.1414813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.72413.0536997
X-RAY DIFFRACTIONr_long_range_B_refined10.1863.739490
X-RAY DIFFRACTIONr_long_range_B_other10.17963.749491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 318 -
Rwork0.406 2981 -
obs--95.98 %

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