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- PDB-1dxo: Crystal structure of human NAD[P]H-QUINONE oxidoreductase CO with... -

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Basic information

Entry
Database: PDB / ID: 1dxo
TitleCrystal structure of human NAD[P]H-QUINONE oxidoreductase CO with 2,3,5,6,tetramethyl-P-benzoquinone (duroquinone) at 2.5 Angstrom resolution
ComponentsQUINONE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / ROSSMANN FOLD
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
DUROQUINONE / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsFaig, M. / Bianchet, M.A. / Chen, S. / Winski, S. / Ross, D. / Amzel, L.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structures of Recombinant Mouse and Human Nad(P)H:Quinone Oxidoreductases:Species Comparison and Structural Changes with Substrate Binding and Release
Authors: Faig, M. / Bianchet, M.A. / Chen, S. / Winski, S. / Ross, D. / Talalay, P. / Amzel, L.M.
#1: Journal: Biochem.Soc.Trans. / Year: 1999
Title: Structure and Mechanism of Cytosolic Quinone Reductase
Authors: Bianchet, M.A. / Foster, C. / Faig, M. / Talalay, P. / Amzel, L.M.
#2: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Human Quinone Reductase Type 2, a Metalloprotein
Authors: Foster, C. / Bianchet, M.A. / Talalay, P. / Zhao, Q. / Amzel, L.M.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: The Three-Dimensional Structure of Nad(P)H:Quinone Reductase, a Flavoprotein Involved in Cancer Chemoprotection and Chemotherapy: Mechanism of Two-Electron Reduction
Authors: Li, R. / Bianchet, M.A. / Talalay, P. / Amzel, L.M.
History
DepositionJan 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS ... SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET IN CHAIN A SHEETS B AND B1 REPRESENT ONE BIFURCATED SHEET IN CHAIN D SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET IN CHAIN C SHEETS D AND D1 REPRESENT ONE BIFURCATED SHEET IN CHAIN D

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QUINONE REDUCTASE
B: QUINONE REDUCTASE
C: QUINONE REDUCTASE
D: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,90512
Polymers123,1064
Non-polymers3,7998
Water1,892105
1
B: QUINONE REDUCTASE
D: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4526
Polymers61,5532
Non-polymers1,9004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-63.7 kcal/mol
Surface area21280 Å2
MethodPISA
2
A: QUINONE REDUCTASE
C: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4526
Polymers61,5532
Non-polymers1,9004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-60.4 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.579, 56.912, 97.755
Angle α, β, γ (deg.)76.24, 76.73, 86.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
QUINONE REDUCTASE / DT-DIAPHORASE


Mass: 30776.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15559, EC: 1.6.99.2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-DQN / DUROQUINONE


Mass: 164.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
225 mMTris-HCl1drop
30.005 mMFAD1drop
430 %PEG33501reservoir
5200 mMsodium acetate1reservoir
6100 mg/mlsodium tricine1reservoir
70.012-0.024 mMFAD1reservoir
88.9 mMduroquinone1reservoir
90.025 mMNADH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→27.66 Å / Num. obs: 36969 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.093
Reflection
*PLUS
Rmerge(I) obs: 0.044

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.5→27.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 411877.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2802 10.1 %RANDOM
Rwork0.202 ---
obs0.202 27730 70.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19 Å2 / ksol: 0.30878 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-2.88 Å23.5 Å2
2---1.82 Å2-0.02 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8692 0 260 105 9057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 190 9.6 %
Rwork0.264 1784 -
obs--30 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NEWPARAM.DQNION.TOP
X-RAY DIFFRACTION3NEWFAD_XPLOR.PARPROTEIN.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMDNA-RNA.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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