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- PDB-4qof: Crystal structure of fmn quinone reductase 2 AT 1.55A -

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Basic information

Entry
Database: PDB / ID: 4qof
TitleCrystal structure of fmn quinone reductase 2 AT 1.55A
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE FLAVOPROTEIN / Flavin MonoNucleotide
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 MONONUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSerriere, J. / Boutin, J.A. / Isabet, T. / Antoine, M. / Ferry, G.
Citation
Journal: To be Published
Title: Crystal structure of FMN quinone reductase 2 at 1.55A
Authors: Serriere, J. / Boutin, J.A. / Isabet, T. / Antoine, M. / Ferry, G.
#1: Journal: Biochem.J. / Year: 2008
Title: Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2.
Authors: Calamini, B. / Santarsiero, B.D. / Boutin, J.A. / Mesecar, A.D.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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)53,0056
Polymers51,9612
Non-polymers1,0444
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-35 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.170, 83.270, 106.440
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
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: 0.9 / Wavelength: 0.9997 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.99971
ReflectionResolution: 1.5→22.69 Å / Num. all: 72946 / Num. obs: 72946 / % possible obs: 99.75 %
Reflection shellResolution: 1.55→1.64 Å / Mean I/σ(I) obs: 1.66 / Num. unique all: 11338 / % possible all: 96.6

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
BUSTER2.11.5refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QWX

2qwx


Resolution: 1.55→22.69 Å / Cor.coef. Fo:Fc: 0.9253 / Cor.coef. Fo:Fc free: 0.9137 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 3647 5 %RANDOM
Rwork0.2139 ---
obs0.215 72946 99.75 %-
all-73162 --
Displacement parametersBiso mean: 24.63 Å2
Baniso -1Baniso -2Baniso -3
1--4.8627 Å20 Å20 Å2
2---2.7365 Å20 Å2
3---7.5992 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.55→22.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 64 388 4082
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014046HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975550HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1360SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes641HARMONIC5
X-RAY DIFFRACTIONt_it4046HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.65
X-RAY DIFFRACTIONt_other_torsion16.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion502SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5248SEMIHARMONIC4
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3282 267 5 %
Rwork0.3221 5073 -
all0.3224 5340 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
100.37370.23880.37440.36142.15040.0068-0.1061-0.0853-0.00230.0727-0.0112-0.14010.0807-0.0795-0.24910.02380.008-0.3285-0.0009-0.16479.84857.856326.2782
20.0138-0.718-0.144700.29053.73180.0420.138-0.0641-0.11850.11-0.0714-0.47390.1676-0.1519-0.17640.01570.0359-0.3710.0027-0.187611.85878.56483.7271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 230
2X-RAY DIFFRACTION2{ B|* }B3 - 230

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