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- PDB-1h66: CRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE CO WITH... -

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Basic information

Entry
Database: PDB / ID: 1h66
TitleCRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE CO WITH 2,5-diaziridinyl-3-hydroxyl-6-methyl-1,4-benzoquinone
ComponentsNAD(P)H DEHYDROGENASE [QUINONE] 1
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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-RH1 / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFaig, M. / Bianchet, M.A. / Winski, S. / Ross, D. / Amzel, L.M.
Citation
Journal: Structure / Year: 2001
Title: Structure-Based Development of Anticancer Drugs: Complexes of Nad(P)H:Quinone Oxidoreductase 1 with Chemotherapeutic Quinones
Authors: Faig, M. / Bianchet, M.A. / Winski, S. / Hargreaves, R. / Moody, C.J. / Hudnott, A.R. / Ross, D. / Amzel, L.M.
#1: 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.
#2: 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.
#3: 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.
#4: 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
DepositionJun 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 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

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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)127,07312
Polymers122,9934
Non-polymers4,0798
Water12,629701
1
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5366
Polymers61,4972
Non-polymers2,0404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-38.9 kcal/mol
Surface area21120 Å2
MethodPISA
2
B: NAD(P)H DEHYDROGENASE [QUINONE] 1
D: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5366
Polymers61,4972
Non-polymers2,0404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-40.9 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.185, 57.080, 97.323
Angle α, β, γ (deg.)77.05, 77.07, 87.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NAD(P)H DEHYDROGENASE [QUINONE] 1 / QUINONE REDUCTASE 1 / QR1 / DT-DIAPHORASE / DTD / AZOREDUCTASE / PHYLLOQUINONE REDUCTASE / MENADIONE REDUCTASE


Mass: 30748.361 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-RH1 / 2,5-DIAZIRIDIN-1-YL-3-(HYDROXYMETHYL)-6-METHYLCYCLOHEXA-2,5-DIENE-1,4-DIONE


Mass: 234.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O3
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Faig, M., (2000) Proc.Natl.Acad.Sci.USA, 97, 3177.
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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: BRANDEIS CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.96 Å / Num. obs: 73718 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.09
Reflection
*PLUS
Redundancy: 3.9 % / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 83.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.96 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 478391.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.199 66309 90 %RANDOM
Rwork0.256 ---
obs0.256 73717 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.4807 Å2 / ksol: 0.343615 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-1.64 Å23.71 Å2
2---2.92 Å22.37 Å2
3---2.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8692 0 280 701 9673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d22.1
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_it0.741.5
X-RAY DIFFRACTIONc_mcangle_it1.312
X-RAY DIFFRACTIONc_scbond_it1.082
X-RAY DIFFRACTIONc_scangle_it1.742.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 9822 90.2 %
Rwork0.301 1070 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2RH1.PARION.TOP
X-RAY DIFFRACTION3NEWFAD_XPLOR.PARPROTEIN.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION5WATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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