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- PDB-4qog: Crystal structure of fad quinone reductase 2 in complex with mela... -

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Basic information

Entry
Database: PDB / ID: 4qog
TitleCrystal structure of fad quinone reductase 2 in complex with melatonin at 1.4A
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE FLAVOPROTEIN / FAD MELATONIN
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 / N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSerriere, J. / Boutin, J.A. / Isabet, T. / Antoine, M. / Ferry, G.
CitationJournal: To be Published
Title: Crystal structure of fad quinone reductase 2 in complex with melatonin at 1.4A
Authors: Serriere, J. / Boutin, J.A. / Isabet, T. / Antoine, M. / Ferry, G.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / 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 / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _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_label_asym_id / _struct_ref_seq_dif.details / _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: Ribosyldihydronicotinamide dehydrogenase [quinone]
B: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1288
Polymers51,9612
Non-polymers2,1666
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-18 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.560, 83.400, 106.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosyldihydronicotinamide dehydrogenase [quinone] / NRH dehydrogenase [quinone] 2 / NRH:quinone oxidoreductase 2 / Quinone reductase 2 / QR2


Mass: 25980.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P16083, EC: 1.10.99.2
#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-ML1 / N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Melatonin


Mass: 232.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES PH7, 1.4M AmSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9997 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 1.4→46.81 Å / Num. all: 93437 / Num. obs: 93437 / % possible obs: 97.95 %
Reflection shellResolution: 1.4→1.48 Å / Mean I/σ(I) obs: 1.61 / Num. unique all: 14884 / % possible all: 92.6

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QWX

2qwx


Resolution: 1.4→46.81 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.38 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22506 4918 5 %RANDOM
Rwork0.19127 ---
obs0.19295 93437 97.95 %-
all-98356 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 142 360 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0194128
X-RAY DIFFRACTIONr_bond_other_d0.0010.023761
X-RAY DIFFRACTIONr_angle_refined_deg2.4811.9275644
X-RAY DIFFRACTIONr_angle_other_deg1.0538686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81824.199181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22415649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4181516
X-RAY DIFFRACTIONr_chiral_restr0.1470.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215215
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02993
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6078.1681947
X-RAY DIFFRACTIONr_mcbond_other2.6068.1671948
X-RAY DIFFRACTIONr_mcangle_it3.362469
X-RAY DIFFRACTIONr_mcangle_other3.3512461
X-RAY DIFFRACTIONr_scbond_it3.1372.1622181
X-RAY DIFFRACTIONr_scbond_other3.1362.1632182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3693.1353176
X-RAY DIFFRACTIONr_long_range_B_refined6.2635399
X-RAY DIFFRACTIONr_long_range_B_other6.2635400
X-RAY DIFFRACTIONr_rigid_bond_restr5.9053180
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded41.6875174
LS refinement shellResolution: 1.398→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 319 -
Rwork0.325 6071 -
obs--87.12 %

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