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- PDB-6rs4: Structure of tabersonine synthase - an alpha-beta hydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 6rs4
TitleStructure of tabersonine synthase - an alpha-beta hydrolase from Catharanthus roseus
ComponentsTabersonine synthase
KeywordsHYDROLASE / alkaloid / TABERSONINE / natural product / biosynthesis / alpha/beta hydrolase fold
Function / homology
Function and homology information


Lyases / alkaloid metabolic process / lyase activity / hydrolase activity / nucleus / cytosol
Similarity search - Function
: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Tabersonine synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCaputi, L. / Franke, J. / Bussey, K. / Farrow, S.C. / Curcino Vieira, I.J. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E.
Funding support Belgium, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council788301 Belgium
Biotechnology and Biological Sciences Research CouncilBB/P012523/1 United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural basis of cycloaddition in biosynthesis of iboga and aspidosperma alkaloids.
Authors: Caputi, L. / Franke, J. / Bussey, K. / Farrow, S.C. / Vieira, I.J.C. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tabersonine synthase
B: Tabersonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,19513
Polymers72,5122
Non-polymers68311
Water12,592699
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint10 kcal/mol
Surface area24240 Å2
Unit cell
Length a, b, c (Å)56.485, 108.962, 63.235
Angle α, β, γ (deg.)90.000, 108.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tabersonine synthase / Hydrolase 2 / CrHL2


Mass: 36256.051 Da / Num. of mol.: 2
Mutation: Native N-terminal MET is replaced by a GLY-PRO dipeptide left over from cleavage of the affinity tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Gene: TS, HL2 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLUBL21 / References: UniProt: A0A2P1GIW3, Lyases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: NULL / PH range: NULL / Temp details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→59.95 Å / Num. obs: 177427 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 10.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.046 / Rrim(I) all: 0.12 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.326.51.685695087740.5150.7081.8261.399.9
7.12-59.956.30.05709711200.9960.0220.05538.699.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDS20160517data reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.25data extraction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7R

2o7r


Resolution: 1.3→59.95 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.907 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 8863 5 %RANDOM
Rwork0.1328 ---
obs0.1342 168522 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.48 Å2 / Biso mean: 16.166 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-0.73 Å2
2--1.8 Å20 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 1.3→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 56 721 5745
Biso mean--28.49 33 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174931
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.6397475
X-RAY DIFFRACTIONr_angle_other_deg1.5061.5711481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77423.271266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62415862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1141520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021169
X-RAY DIFFRACTIONr_rigid_bond_restr7.269310394
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 689 -
Rwork0.281 12394 -
all-13083 -
obs--99.82 %

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