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- PDB-3tzb: Quinone Oxidoreductase (NQ02) bound to NSC13000 -

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Basic information

Entry
Database: PDB / ID: 3tzb
TitleQuinone Oxidoreductase (NQ02) bound to NSC13000
ComponentsRibosyldihydronicotinamide dehydrogenase [quinone]
KeywordsOXIDOREDUCTASE / FAD
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
9-AMINOACRIDINE / FLAVIN-ADENINE DINUCLEOTIDE / Ribosyldihydronicotinamide dehydrogenase [quinone]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1901 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: Mol.Cancer Ther. / Year: 2012
Title: In silico screening reveals structurally diverse, nanomolar inhibitors of NQO2 that are functionally active in cells and can modulate NF-kappa B signaling.
Authors: Nolan, K.A. / Dunstan, M.S. / Caraher, M.C. / Scott, K.A. / Leys, D. / Stratford, I.J.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: 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_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]
C: Ribosyldihydronicotinamide dehydrogenase [quinone]
D: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,59416
Polymers103,4104
Non-polymers4,18512
Water6,720373
1
A: Ribosyldihydronicotinamide dehydrogenase [quinone]
B: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7978
Polymers51,7052
Non-polymers2,0926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-22 kcal/mol
Surface area18610 Å2
MethodPISA
2
C: Ribosyldihydronicotinamide dehydrogenase [quinone]
D: Ribosyldihydronicotinamide dehydrogenase [quinone]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7978
Polymers51,7052
Non-polymers2,0926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-22 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.620, 62.101, 78.506
Angle α, β, γ (deg.)92.950, 90.100, 110.450
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25852.404 Da / Num. of mol.: 4
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-AA / 9-AMINOACRIDINE / 9-Aminoacridine


Mass: 195.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H11N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→28.2 Å / Num. all: 42549 / Num. obs: 42485 / % possible obs: 92 % / Redundancy: 1.8 % / Rsym value: 0.085 / Net I/σ(I): 12.9
Reflection shellResolution: 1.45→1.51 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 4.38 / Rsym value: 0.371 / % possible all: 90.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1901→28.2 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.98 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 2148 5.06 %
Rwork0.1673 --
obs0.1706 42485 92.3 %
all-42549 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.318 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 191.1 Å2 / Biso mean: 31.3634 Å2 / Biso min: 3.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.9785 Å20.621 Å20.3875 Å2
2--0.4145 Å2-0.1393 Å2
3---0.5639 Å2
Refinement stepCycle: LAST / Resolution: 2.1901→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 276 373 7911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077762
X-RAY DIFFRACTIONf_angle_d1.10710578
X-RAY DIFFRACTIONf_chiral_restr0.0711116
X-RAY DIFFRACTIONf_plane_restr0.0051308
X-RAY DIFFRACTIONf_dihedral_angle_d21.0192862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1901-2.2410.27671410.20192670281192
2.241-2.2970.25881400.19092735287593
2.297-2.35910.31221400.18982718285895
2.3591-2.42850.30391550.20122789294495
2.4285-2.50690.28291400.19842759289994
2.5069-2.59640.27441220.19172733285593
2.5964-2.70030.30661560.19522704286094
2.7003-2.82310.31921370.18852758289593
2.8231-2.97190.30871440.19992658280292
2.9719-3.15790.26821360.18892683281992
3.1579-3.40150.25621420.17292617275990
3.4015-3.74330.18661370.14962585272289
3.7433-4.28380.17661600.12872586274689
4.2838-5.39290.15651500.11982599274990
5.3929-31.68770.17121480.15172743289194
Refinement TLS params.Method: refined / Origin x: 6.2309 Å / Origin y: 23.1078 Å / Origin z: 22.5613 Å
111213212223313233
T0.0131 Å2-0.0044 Å2-0.0089 Å2-0.0274 Å20.0034 Å2--0.03 Å2
L0.0479 °2-0.0607 °2-0.1215 °2-0.1324 °20.1222 °2--0.3896 °2
S-0.0112 Å °-0.0028 Å °-0.0154 Å °-0.0003 Å °-0.0035 Å °0.0091 Å °-0.0065 Å °0.0027 Å °0.013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 229
2X-RAY DIFFRACTION1allB2 - 229
3X-RAY DIFFRACTION1allC0 - 229
4X-RAY DIFFRACTION1allD2 - 229
5X-RAY DIFFRACTION1allA231 - 501
6X-RAY DIFFRACTION1allB231 - 501
7X-RAY DIFFRACTION1allC231 - 501
8X-RAY DIFFRACTION1allD231 - 501

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