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- PDB-1d4a: CRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AT 1.7 ... -

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Basic information

Entry
Database: PDB / ID: 1d4a
TitleCRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AT 1.7 A 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
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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 human and mouse NAD(P)H:quinone oxidoreductases: species comparison and structural changes with substrate binding and release.
Authors: Faig, M. / Bianchet, M.A. / Talalay, P. / Chen, S. / Winski, S. / Ross, D. / 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: 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.
#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.
History
DepositionOct 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 7, 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: QUINONE REDUCTASE
B: QUINONE REDUCTASE
C: QUINONE REDUCTASE
D: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2488
Polymers123,1064
Non-polymers3,1424
Water10,665592
1
A: QUINONE REDUCTASE
C: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1244
Polymers61,5532
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-50 kcal/mol
Surface area21390 Å2
MethodPISA
2
B: QUINONE REDUCTASE
D: QUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1244
Polymers61,5532
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-55 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.678, 57.032, 97.402
Angle α, β, γ (deg.)77.04, 76.72, 86.89
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % PEG 3350 200 MM NAACETATE 12-24 MICROM FAD 100MM NA-TRICINE PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8
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: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→43.44 Å / Num. all: 98473 / Num. obs: 30063 / % possible obs: 78.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 4.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.159 / % possible all: 24.2
Reflection
*PLUS
Num. obs: 98473 / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.7→43.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1344082.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 9755 9.9 %RANDOM
Rwork0.209 ---
obs0.209 98473 78.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.23 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-2.75 Å23.45 Å2
2---1.12 Å24.46 Å2
3---1.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.7→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8692 0 212 592 9496
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_deg1.3
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_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.831.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it1.172
X-RAY DIFFRACTIONc_scangle_it1.832.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 504 9.4 %
Rwork0.313 4852 -
obs--25.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD_XPLOR
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.313

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