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- PDB-6rj8: Structure of the alpha-beta hydrolase CorS from Tabernathe iboga -

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Basic information

Entry
Database: PDB / ID: 6rj8
TitleStructure of the alpha-beta hydrolase CorS from Tabernathe iboga
Componentsalpha-beta hydrolase CorS
KeywordsHYDROLASE / alkaloid / iboga / coronaridine / natural product / biosynthesis / alpha/beta hydrolase fold
Function / homology: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / Coronaridine synthase
Function and homology information
Biological speciesTabernanthe iboga (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsFarrow, S.C. / Caputi, L. / Kamileen, M.O. / Bussey, K. / Stevenson, C.E.M. / Mundy, J. / 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
DepositionApr 26, 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:
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Assembly

Deposited unit
A: alpha-beta hydrolase CorS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2849
Polymers36,4791
Non-polymers8058
Water6,251347
1
A: alpha-beta hydrolase CorS
hetero molecules

A: alpha-beta hydrolase CorS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,56818
Polymers72,9592
Non-polymers1,61016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area5770 Å2
ΔGint22 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.838, 82.838, 247.556
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-638-

HOH

31A-790-

HOH

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Components

#1: Protein alpha-beta hydrolase CorS


Mass: 36479.258 Da / Num. of mol.: 1
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.) Tabernanthe iboga (plant) / Gene: corS / Details (production host): POPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLUBL21
References: UniProt: A0A5B8X6B5*PLUS, 2-hydroxyisoflavanone dehydratase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.42→71.74 Å / Num. obs: 95612 / % possible obs: 100 % / Redundancy: 37.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.023 / Rrim(I) all: 0.142 / Net I/σ(I): 10.4 / Num. measured all: 3543087 / Scaling rejects: 2968
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.42-1.4437.81.7617539946460.9260.2871.7842.3
7.78-71.7428.70.06217617570.9990.0110.06115.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALS1.5.0data reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7R

2o7r


Resolution: 1.42→71.74 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.821 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 4757 5 %RANDOM
Rwork0.1544 ---
obs0.1557 90713 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.68 Å2 / Biso mean: 18.725 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 1.42→71.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 53 353 2897
Biso mean--38.62 32.94 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132666
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172435
X-RAY DIFFRACTIONr_angle_refined_deg1.51.643615
X-RAY DIFFRACTIONr_angle_other_deg1.4051.5735660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1775329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57222.362127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61615413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3831512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02569
X-RAY DIFFRACTIONr_rigid_bond_restr1.58435098
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 340 -
Rwork0.211 6590 -
all-6930 -
obs--99.81 %

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