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- PDB-9qsw: Crystal structure of an NtA622L variant in complex with NADP+ and... -

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Basic information

Entry
Database: PDB / ID: 9qsw
TitleCrystal structure of an NtA622L variant in complex with NADP+ and Nicotinic acid
ComponentsIsoflavone reductase homolog A622-like
KeywordsPLANT PROTEIN / Oxidoreductase / Nicotine / Niacin / NADPH / Rossmann-fold / IFR-like / PIP-reductase
Function / homology
Function and homology information


nicotine biosynthetic process / lignan biosynthetic process / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / alkaloid metabolic process / secondary metabolite biosynthetic process / cytoplasm
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NICOTINIC ACID / Isoflavone reductase homolog A622-like
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMokos, D. / Daniel, B.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundP34337 Austria
Austrian Science FundDOC46 Austria
Austrian Science FundDOC130 Austria
CitationJournal: To Be Published
Title: A622: A key oxidoreductase in the Nicotine biosynthesis
Authors: Mokos, D. / Leitner, D. / Schruefer, A. / Grubmueller, S. / Reisz, C. / Juric, J. / Berger, T. / Singh, A. / Friess, M. / Breinbauer, R. / Gruber, K. / Daniel, B.
History
DepositionApr 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoflavone reductase homolog A622-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5073
Polymers34,6411
Non-polymers8672
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint3 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.026, 63.353, 61.088
Angle α, β, γ (deg.)90, 105.679, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoflavone reductase homolog A622-like / NtA622L


Mass: 34640.734 Da / Num. of mol.: 1 / Mutation: K99N M201I M259L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: A622L, IRL2 / Production host: Escherichia coli (E. coli)
References: UniProt: B6VRE6, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.05 M Tris pH 8.5, 1.0 M Ammonium sulfate, 5 mM Nicotinic acid, 5 mg/ml protein (Index HT screen condition 6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03272 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03272 Å / Relative weight: 1
ReflectionResolution: 1.68→43.104 Å / Num. obs: 34175 / % possible obs: 98.6 % / Redundancy: 6.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.113 / Rrim(I) all: 0.212 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.02-43.16.30.082380.9920.050.095
1.68-1.76.61.68516660.5361.0732.006

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→43.104 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.509 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.22 1763 5.195 %
Rwork0.1795 32176 -
all0.182 --
obs-33939 98.517 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.234 Å2
Baniso -1Baniso -2Baniso -3
1-1.571 Å20 Å20.367 Å2
2---1.261 Å20 Å2
3----0.446 Å2
Refinement stepCycle: LAST / Resolution: 1.68→43.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 57 123 2597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122531
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162423
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.8273444
X-RAY DIFFRACTIONr_angle_other_deg0.8571.7515601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2585305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.496510
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg19.34952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44910434
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.0410106
X-RAY DIFFRACTIONr_chiral_restr0.1190.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022851
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02541
X-RAY DIFFRACTIONr_nbd_refined0.2090.2502
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.22308
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21289
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2110
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.27
X-RAY DIFFRACTIONr_nbd_other0.1520.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.29
X-RAY DIFFRACTIONr_mcbond_it3.0092.3491223
X-RAY DIFFRACTIONr_mcbond_other3.0012.3481223
X-RAY DIFFRACTIONr_mcangle_it4.334.2131527
X-RAY DIFFRACTIONr_mcangle_other4.334.2161528
X-RAY DIFFRACTIONr_scbond_it4.6382.9021308
X-RAY DIFFRACTIONr_scbond_other4.6412.91306
X-RAY DIFFRACTIONr_scangle_it7.0585.0611917
X-RAY DIFFRACTIONr_scangle_other7.0565.061918
X-RAY DIFFRACTIONr_lrange_it8.73225.0162855
X-RAY DIFFRACTIONr_lrange_other8.70924.4262831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.68-1.7240.3051230.28423680.28525380.9210.93698.14810.273
1.724-1.7710.31140.25922390.26124550.9310.95295.84520.247
1.771-1.8220.2231310.22422510.22424020.9670.96399.16740.208
1.822-1.8780.2531170.19222220.19523530.9590.97399.4050.178
1.878-1.9390.2411180.1921090.19222390.9620.97699.46410.177
1.939-2.0070.198850.17420840.17521790.9740.98199.54110.162
2.007-2.0830.1951030.16519940.16621130.9770.98299.24280.154
2.083-2.1680.2241370.16818880.17120470.9690.98298.92530.157
2.168-2.2640.1931230.16818160.1719600.9760.9898.92860.158
2.264-2.3740.2141010.16817300.17118570.9630.98198.59990.161
2.374-2.5020.221780.16315840.16617620.970.98294.32460.156
2.502-2.6530.258830.1715970.17416940.9620.98199.17360.168
2.653-2.8360.208800.1714840.17215780.9740.98299.11280.172
2.836-3.0620.193830.16813850.1714760.9780.98299.4580.174
3.062-3.3520.236570.17313120.17513730.9640.98199.70870.184
3.352-3.7450.194580.16811770.16912410.9720.98299.51650.184
3.745-4.3190.242520.16310200.16710820.9680.98399.07580.186
4.319-5.2770.196550.1698220.1719330.9780.98293.99790.191
5.277-7.4070.235340.1946900.1957290.9730.97799.31410.216
7.407-43.1040.214310.2183910.2184250.9840.98399.29410.236

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