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- PDB-2qr2: HUMAN QUINONE REDUCTASE TYPE 2, COMPLEX WITH MENADIONE -

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Basic information

Entry
Database: PDB / ID: 2qr2
TitleHUMAN QUINONE REDUCTASE TYPE 2, COMPLEX WITH MENADIONE
ComponentsPROTEIN (QUINONE REDUCTASE TYPE 2)
KeywordsOXIDOREDUCTASE / QUINONE-REDUCTASE (CYTOSOLIC) / FLAVOPROTEIN / METALLOENZYME
Function / homology
Function and homology information


ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / electron transfer activity / oxidoreductase activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / 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 / MENADIONE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsFoster, C. / Bianchet, M.A. / Talalay, P. / Amzel, L.M.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal structure of human quinone reductase type 2, a metalloflavoprotein.
Authors: Foster, C.E. / Bianchet, M.A. / Talalay, P. / Zhao, Q. / Amzel, L.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Unexpected genetic and structural relationships of a long-forgotten flavoenzyme to NAD(P)H:quinone reductase (DT-diaphorase)
Authors: Zhao, Q. / Yang, X.L. / Holtzclaw, W.D. / Talalay, P.
History
DepositionApr 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PROTEIN (QUINONE REDUCTASE TYPE 2)
B: PROTEIN (QUINONE REDUCTASE TYPE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7458
Polymers51,6992
Non-polymers2,0466
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-41 kcal/mol
Surface area17890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.600, 106.270, 56.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.759812, 0.00496, -0.650124), (0.005088, -0.999986, -0.001683), (-0.650123, -0.002029, -0.759826)
Vector: 19.191, 30.2815, 52.0138)

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Components

#1: Protein PROTEIN (QUINONE REDUCTASE TYPE 2) / MENADIONE REDUCTASE


Mass: 25849.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC GENE / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): NQO2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P16083, EC: 1.6.99.2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-VK3 / MENADIONE / VITAMIN K3 / 2-METHYL-1,4-NAPHTHALENEDIONE


Mass: 172.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE IS IN ERROR AT RESIDUE 140, CYS. THE CORRECT RESIDUE IS GLY. (RESIDUE 139 IN ...THE SEQUENCE DATABASE IS IN ERROR AT RESIDUE 140, CYS. THE CORRECT RESIDUE IS GLY. (RESIDUE 139 IN THE COORDINATES.)

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.200 mMmenadione1drop
21.66 Mammonium sulfate1reservoir
310 mMsodium HEPES1reservoir
40.012 mMFAD1reservoir
55 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1998 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→100 Å / Num. obs: 18052 / % possible obs: 97.6 % / Redundancy: 5.6 % / Rsym value: 0.085 / Net I/σ(I): 23
Reflection shellResolution: 2.45→2.56 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.465 / % possible all: 85.8
Reflection
*PLUS
Num. measured all: 101551 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 85.8 % / Rmerge(I) obs: 0.465

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→6 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1774 10 %RANDOM
Rwork0.218 ---
obs-26074 77.4 %-
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.45→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 134 149 3931
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_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.45→2.5 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.373 80 10 %
Rwork0.334 462 -
obs--82.04 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11X.DNATOPH11.WAT
X-RAY DIFFRACTION3PARAM11.WAT
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_scbond_it2.5
LS refinement shell
*PLUS
Lowest resolution: 2.5 Å / Rfactor Rfree: 0.373 / % reflection Rfree: 10 % / Rfactor Rwork: 0.334

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