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- PDB-7quj: Structure of NsNEPS2, a 7S-cis-trans nepetalactone synthase -

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Basic information

Entry
Database: PDB / ID: 7quj
TitleStructure of NsNEPS2, a 7S-cis-trans nepetalactone synthase
ComponentsNsNEPS2
KeywordsBIOSYNTHETIC PROTEIN / SDR / Cyclisation / Oxidation / NAD+
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesNepeta sibirica (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHernandez Lozada, N.J. / Hong, B. / Wood, J.C. / Caputi, L. / Basquin, J. / Chuang, L. / Kunert, M. / Rodriguez Lopez, C.R. / Langley, C. / Zhao, D. ...Hernandez Lozada, N.J. / Hong, B. / Wood, J.C. / Caputi, L. / Basquin, J. / Chuang, L. / Kunert, M. / Rodriguez Lopez, C.R. / Langley, C. / Zhao, D. / Buell, C.R. / Lichman, B.R. / O'Connor, S.E.
Funding support United States, European Union, Germany, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1444499 United States
European Research Council (ERC)788301European Union
Alexander von Humboldt Foundation Germany
CitationJournal: Nat Commun / Year: 2022
Title: Biocatalytic routes to stereo-divergent iridoids.
Authors: Hernandez Lozada, N.J. / Hong, B. / Wood, J.C. / Caputi, L. / Basquin, J. / Chuang, L. / Kunert, M. / Rodriguez Lopez, C.E. / Langley, C. / Zhao, D. / Buell, C.R. / Lichman, B.R. / O'Connor, S.E.
History
DepositionJan 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NsNEPS2
B: NsNEPS2
C: NsNEPS2
D: NsNEPS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2468
Polymers119,5934
Non-polymers2,6544
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17360 Å2
ΔGint-134 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.753, 106.680, 142.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
NsNEPS2


Mass: 29898.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nepeta sibirica (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium acetate with 11.5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→49.54 Å / Num. obs: 88386 / % possible obs: 97.81 % / Redundancy: 12.2 % / Biso Wilson estimate: 36.45 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.3
Reflection shellResolution: 1.85→1.916 Å / Rmerge(I) obs: 0.775 / Num. unique obs: 7393 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9Q

6f9q


Resolution: 1.85→49.54 Å / SU ML: 0.2111 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.3892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 8499 5.01 %
Rwork0.1709 161260 -
obs0.1724 88386 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7476 0 176 538 8190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00827756
X-RAY DIFFRACTIONf_angle_d1.051410516
X-RAY DIFFRACTIONf_chiral_restr0.06051260
X-RAY DIFFRACTIONf_plane_restr0.00731336
X-RAY DIFFRACTIONf_dihedral_angle_d7.54911116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.40352170.34094149X-RAY DIFFRACTION75.38
1.87-1.890.36592410.31484618X-RAY DIFFRACTION83.07
1.89-1.910.28492520.28194752X-RAY DIFFRACTION86.6
1.91-1.940.30442640.25885056X-RAY DIFFRACTION92.22
1.94-1.960.25892750.2315257X-RAY DIFFRACTION95.3
1.96-1.990.24542850.21485463X-RAY DIFFRACTION99.02
1.99-2.020.23832870.20285488X-RAY DIFFRACTION99.98
2.02-2.050.24432860.20315503X-RAY DIFFRACTION99.86
2.05-2.080.20732970.19335494X-RAY DIFFRACTION99.93
2.08-2.120.2472830.19565503X-RAY DIFFRACTION99.95
2.12-2.150.24162920.19485545X-RAY DIFFRACTION99.93
2.15-2.190.22212900.18645442X-RAY DIFFRACTION99.93
2.19-2.230.24412940.18935540X-RAY DIFFRACTION100
2.23-2.280.21672850.18525463X-RAY DIFFRACTION100
2.28-2.330.21782940.18145481X-RAY DIFFRACTION100
2.33-2.380.21262930.18125531X-RAY DIFFRACTION99.98
2.38-2.440.2082880.17435541X-RAY DIFFRACTION99.98
2.44-2.510.20362840.18075463X-RAY DIFFRACTION100
2.51-2.580.21442950.1875501X-RAY DIFFRACTION99.97
2.58-2.670.22332890.19375492X-RAY DIFFRACTION99.97
2.67-2.760.25872900.19265508X-RAY DIFFRACTION99.97
2.76-2.870.21492930.18925506X-RAY DIFFRACTION99.91
2.87-30.2152850.18215507X-RAY DIFFRACTION99.95
3-3.160.2172890.18275491X-RAY DIFFRACTION99.83
3.16-3.360.20672940.17915493X-RAY DIFFRACTION99.93
3.36-3.620.17712880.175522X-RAY DIFFRACTION99.98
3.62-3.980.19872910.14935491X-RAY DIFFRACTION99.95
3.98-4.560.13762920.13165498X-RAY DIFFRACTION99.98
4.56-5.740.16872980.14495493X-RAY DIFFRACTION99.9
5.74-49.540.17142880.14815469X-RAY DIFFRACTION99.46

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