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- PDB-4cet: Crystal structure of the complex of the P187S variant of human NA... -

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Basic information

Entry
Database: PDB / ID: 4cet
TitleCrystal structure of the complex of the P187S variant of human NAD(P) H:quinone oxidoreductase with dicoumarol at 2.2 A resolution
ComponentsNAD(P)H DEHYDROGENASE [QUINONE] 1
KeywordsOXIDOREDUCTASE / COUMARIN-BASED INHIBITORS / NQ01 / FAD / FLAVOPROTEIN / NAD / NADP / NADPH / OXIDOREDUCTASE-INHIBITOR COMPLEX / SINGLE AMINO ACID EXCHANGE / P187S
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 / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BISHYDROXY[2H-1-BENZOPYRAN-2-ONE,1,2-BENZOPYRONE] / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLienhart, W.D. / Gudipati, V. / Uhl, M.K. / Binter, A. / Pulido, S. / Saf, R. / Zangger, K. / Gruber, K. / Macheroux, P.
CitationJournal: FEBS J. / Year: 2014
Title: Collapse of the Native Structure by a Single Amino Acid Exchange in Human Nad(P)H:Quinone Oxidoreductase (Nqo1).
Authors: Lienhart, W.-D. / Gudipati, V. / Uhl, M.K. / Binter, A. / Pulido, S. / Saf, R. / Zangger, K. / Gruber, K. / Macheroux, P.
History
DepositionNov 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1913
Polymers33,0691
Non-polymers1,1222
Water2,504139
1
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules

A: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3826
Polymers66,1382
Non-polymers2,2444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7400 Å2
ΔGint-40.7 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.050, 51.050, 169.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 / NADPH QUINONE OXIDOREDUCTASE


Mass: 33068.934 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DTC / BISHYDROXY[2H-1-BENZOPYRAN-2-ONE,1,2-BENZOPYRONE] / DICOUMAROL


Mass: 336.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.67 Å3/Da / Density % sol: 26.37 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.005 M CO(II)CL-HEXAHYDRATE, 0.005 M NI(II)CL-HEXAHYDRATE, 0.005 M CDCL-HYDRATE, 0.005 M MGCL-HEAXHYDRATE, 0.1 M HEPES PH 7.5, 12 % PEG-3350 (W/V)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1354
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1354 Å / Relative weight: 1
ReflectionResolution: 2.2→33.8 Å / Num. obs: 12127 / % possible obs: 99.8 % / Observed criterion σ(I): 3.2 / Redundancy: 11.9 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.2 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBG

1qbg


Resolution: 2.2→33.197 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 22.24 / Stereochemistry target values: ML
Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE FIRST 2 AND THE LAST 51 RESIDUES (MISSING C-TERMINAL REGION).
RfactorNum. reflection% reflection
Rfree0.2239 576 4.8 %
Rwork0.1755 --
obs0.178 12065 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 78 139 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041926
X-RAY DIFFRACTIONf_angle_d0.8952626
X-RAY DIFFRACTIONf_dihedral_angle_d15.626699
X-RAY DIFFRACTIONf_chiral_restr0.06273
X-RAY DIFFRACTIONf_plane_restr0.004326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.42160.29551440.22922775X-RAY DIFFRACTION99
2.4216-2.77190.25971340.2072805X-RAY DIFFRACTION100
2.7719-3.49170.24341490.18562853X-RAY DIFFRACTION100
3.4917-33.20060.17851490.14453056X-RAY DIFFRACTION100

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