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- PDB-9qrg: Crystal structure of mutant NtA622L in complex with NADP+ and Nic... -

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Basic information

Entry
Database: PDB / ID: 9qrg
TitleCrystal structure of mutant NtA622L in complex with NADP+ and Nicotinamide
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 / NICOTINAMIDE / Isoflavone reductase homolog A622-like
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 3, 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)35,5525
Polymers34,6411
Non-polymers9124
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-10 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.289, 47.459, 142.623
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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-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
#3: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 3.75 mg/ml purified A119, 0.1 M Sodium formate, 10% w/v Polyethylene glycol 3,350 (Index HT Screen condition 90)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.3→47.46 Å / Num. obs: 64136 / % possible obs: 87.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.017 / Rrim(I) all: 0.033 / Net I/σ(I): 26.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.12-47.464.60.0244820.9980.0170.03
1.3-1.324.30.76215600.6040.5420.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.031 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.678 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1682 3070 4.79 %
Rwork0.1335 61023 -
all0.135 --
obs-64093 87.443 %
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: 25.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.186 Å20 Å2-0 Å2
2---0.12 Å2-0 Å2
3----0.066 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 59 254 2730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122709
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162601
X-RAY DIFFRACTIONr_angle_refined_deg1.911.8273710
X-RAY DIFFRACTIONr_angle_other_deg0.8061.7576012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.382510
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg25.81653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00610474
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.93910113
X-RAY DIFFRACTIONr_chiral_restr0.1090.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023150
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02590
X-RAY DIFFRACTIONr_nbd_refined0.2230.2590
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22412
X-RAY DIFFRACTIONr_nbtor_refined0.180.21326
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2182
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.220
X-RAY DIFFRACTIONr_nbd_other0.1930.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.229
X-RAY DIFFRACTIONr_mcbond_it6.6342.2051317
X-RAY DIFFRACTIONr_mcbond_other6.5482.2051317
X-RAY DIFFRACTIONr_mcangle_it9.063.9841676
X-RAY DIFFRACTIONr_mcangle_other9.0753.9871677
X-RAY DIFFRACTIONr_scbond_it8.6312.5091392
X-RAY DIFFRACTIONr_scbond_other8.6282.5091393
X-RAY DIFFRACTIONr_scangle_it11.9834.4612034
X-RAY DIFFRACTIONr_scangle_other11.984.462035
X-RAY DIFFRACTIONr_lrange_it20.19126.2453192
X-RAY DIFFRACTIONr_lrange_other18.54825.3223136
X-RAY DIFFRACTIONr_rigid_bond_restr3.96635310
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
1.3-1.3340.2831050.26723170.26853820.9570.9645.00190.248
1.334-1.370.2411370.2327050.23151970.9670.97254.68540.205
1.37-1.410.221510.19832790.19950770.9730.97967.55960.168
1.41-1.4530.232010.17339650.17649040.9660.98484.95110.145
1.453-1.5010.1752060.14342830.14547810.9810.98893.89250.117
1.501-1.5540.1762120.12242060.12546230.9820.99195.56570.102
1.554-1.6120.1552200.09841220.10144840.9860.99496.83320.083
1.612-1.6780.1421990.09239870.09443090.9870.99597.14550.078
1.678-1.7520.1381860.09638220.09841440.9880.99496.71810.084
1.752-1.8380.1561970.10136500.10439650.9860.99497.0240.091
1.838-1.9370.1421620.10135330.10337750.9890.99497.88080.095
1.937-2.0540.1531510.10833930.1136040.9850.99498.33520.104
2.054-2.1960.1521700.11231500.11433730.9860.99498.42870.111
2.196-2.3710.131610.10729610.10831640.9910.99498.67260.109
2.371-2.5970.1651310.11526820.11729030.9820.99296.89980.122
2.597-2.9020.141290.12225230.12326690.9870.99199.36310.132
2.902-3.3490.1741390.14221970.14423530.9840.98899.27750.161
3.349-4.0960.1391120.13718910.13720140.9880.98899.45380.163
4.096-5.7680.202710.16214890.16416170.9810.98796.4750.207
5.768-45.0310.41300.2488680.2549580.9450.96693.7370.292

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