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- PDB-1dxq: CRYSTAL STRUCTURE OF MOUSE NAD[P]H-QUINONE OXIDOREDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1dxq
TitleCRYSTAL STRUCTURE OF MOUSE NAD[P]H-QUINONE OXIDOREDUCTASE
ComponentsQUINONE REDUCTASE
KeywordsFLAVOPROTEIN / DT-DIAPHORASE / CANCER / CHEMOPROTECTION / CHEMOTHERAPY / DEHYDROGENASEROSSMAN FOLD / OXIDOREDUCTASE
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / response to caloric restriction / NAD(P)H dehydrogenase (quinone) activity / negative regulation of ferroptosis ...Regulation of ornithine decarboxylase (ODC) / ubiquinone metabolic process / vitamin E metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / vitamin K metabolic process / NADH dehydrogenase (quinone) (non-electrogenic) activity / response to caloric restriction / NAD(P)H dehydrogenase (quinone) activity / negative regulation of ferroptosis / removal of superoxide radicals / cell redox homeostasis / protein catabolic process / negative regulation of protein catabolic process / protein polyubiquitination / response to oxidative stress / cellular response to oxidative stress / response to lipopolysaccharide / innate immune response / 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
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 14, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)126,5448
Polymers123,4024
Non-polymers3,1424
Water00
1
A: QUINONE REDUCTASE
C: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2724
Polymers61,7012
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-62.4 kcal/mol
Surface area26680 Å2
MethodPQS
2
B: QUINONE REDUCTASE
D: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2724
Polymers61,7012
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-50.4 kcal/mol
Surface area26480 Å2
MethodPQS
Unit cell
Length a, b, c (Å)54.960, 171.620, 67.140
Angle α, β, γ (deg.)90.00, 112.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein
QUINONE REDUCTASE / DT-DIAPHORASE / NAD(P)H DEHYDROGENASE [QUINONE] 1 / DTD / AZOREDUCTASE / PHYLLOQUINONE REDUCTASE / ...DT-DIAPHORASE / NAD(P)H DEHYDROGENASE [QUINONE] 1 / DTD / AZOREDUCTASE / PHYLLOQUINONE REDUCTASE / MENADIONE REDUCTASE


Mass: 30850.408 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q64669, 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

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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: 48.19 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: R-AXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→42.98 Å / Num. obs: 18847 / % possible obs: 66.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.1
Reflection
*PLUS
% possible obs: 80 % / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QRD

1qrd


Resolution: 2.8→42.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1633136.18 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.277 916 4.9 %RANDOM
Rwork0.207 ---
obs0.207 18847 66.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.290322 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å20 Å26.84 Å2
2---2.48 Å20 Å2
3----2.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 212 0 8924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 42 4.4 %
Rwork0.308 911 -
obs--18.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD_XPLOR.PARFAD_XPLOR.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_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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