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- PDB-1qrd: QUINONE REDUCTASE/FAD/CIBACRON BLUE/DUROQUINONE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qrd
TitleQUINONE REDUCTASE/FAD/CIBACRON BLUE/DUROQUINONE COMPLEX
ComponentsQUINONE-REDUCTASE
KeywordsQUINONE-REDUCTASE (CYTOSOLIC) / OXIDOREDUCTASE / FLAVOPROTEIN
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / NADH oxidation / cellular response to metal ion ...Regulation of ornithine decarboxylase (ODC) / response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / NADH oxidation / cellular response to metal ion / NADPH oxidation / response to tetrachloromethane / response to hydrogen sulfide / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / response to carbohydrate / response to alkaloid / negative regulation of ferroptosis / superoxide metabolic process / response to amine / response to testosterone / superoxide dismutase activity / response to electrical stimulus / removal of superoxide radicals / response to hormone / cell redox homeostasis / response to nutrient / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / response to organic cyclic compound / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of neuron apoptotic process / response to estradiol / cellular response to oxidative stress / response to ethanol / response to oxidative stress / response to lipopolysaccharide / response to xenobiotic stimulus / innate immune response / neuronal cell body / dendrite / negative regulation of apoptotic process / identical protein binding / nucleus / cytosol / cytoplasm
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
CIBACRON BLUE / DUROQUINONE / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsLi, R. / Bianchet, M.A. / Talalay, P. / Amzel, L.M.
CitationJournal: 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 the two-electron reduction.
Authors: Li, R. / Bianchet, M.A. / Talalay, P. / Amzel, L.M.
History
DepositionJul 28, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: QUINONE-REDUCTASE
B: QUINONE-REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1538
Polymers61,7052
Non-polymers3,4486
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: QUINONE-REDUCTASE
hetero molecules

A: QUINONE-REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1538
Polymers61,7052
Non-polymers3,4486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12070 Å2
ΔGint-113 kcal/mol
Surface area21370 Å2
MethodPISA, PQS
3
B: QUINONE-REDUCTASE
hetero molecules

B: QUINONE-REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1538
Polymers61,7052
Non-polymers3,4486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)72.000, 107.000, 88.400
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein QUINONE-REDUCTASE / DT-DIAPHORASE


Mass: 30852.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus rattus (black rat) / References: UniProt: P05982, EC: 1.6.99.2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CBD / CIBACRON BLUE


Mass: 774.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H20ClN7O11S3
#4: Chemical ChemComp-DQN / DUROQUINONE


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.45 Mammonium sulfate1reservoir
30.5 %PEG80001reservoir
430 mMCibacron blue(pure ring A o-sulfonate)1reservoir
5150 mMimidazole1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 23775 / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Redundancy: 5 %
Reflection
*PLUS
Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2.4→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 21737 88.8 %
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 232 48 4642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_improper_angle_d

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