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- PDB-9y6l: Avermitilol synthase A177S: Complex with Mg, inorganic pyrophosph... -

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Basic information

Entry
Database: PDB / ID: 9y6l
TitleAvermitilol synthase A177S: Complex with Mg, inorganic pyrophosphate, and benzyltriethyl ammonium cation
ComponentsAvermitilol synthase
KeywordsLYASE / Biosynthesis / Terpene / Cyclization
Function / homologyavermitilol synthase / Terpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / metal ion binding / N-benzyl-N,N-diethylethanaminium / DIPHOSPHATE / Avermitilol synthase
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsGaynes, M.N. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2025
Title: Structure and Mechanism of Avermitilol Synthase, a Sesquiterpene Cyclase That Generates a Highly Strained 6-6-3 Tricyclic Alcohol.
Authors: Gaynes, M.N. / Osika, K.R. / Christianson, D.W.
History
DepositionSep 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Avermitilol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3567
Polymers36,8551
Non-polymers5016
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.571, 56.096, 72.693
Angle α, β, γ (deg.)90.000, 125.340, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Avermitilol synthase


Mass: 36854.605 Da / Num. of mol.: 1 / Mutation: A177S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: tpc1, SAV_76 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82RR7, avermitilol synthase

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Non-polymers , 5 types, 202 molecules

#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#3: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 8 mg/mL avermitilol synthase, 0.1 M bis-tris propane (pH 8.5-9.4), 30%PEG 6000, and 0.3-0.5% n-dodecyl-beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.29→29.89 Å / Num. obs: 73659 / % possible obs: 94.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.039 / Net I/σ(I): 9.2
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.912 / Num. unique obs: 2304 / CC1/2: 0.332 / Rpim(I) all: 0.652

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→29.89 Å / SU ML: 0.1436 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1951 2000 2.72 %
Rwork0.1785 71587 -
obs0.179 73587 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.51 Å2
Refinement stepCycle: LAST / Resolution: 1.29→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 30 196 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052572
X-RAY DIFFRACTIONf_angle_d0.88023506
X-RAY DIFFRACTIONf_chiral_restr0.0706372
X-RAY DIFFRACTIONf_plane_restr0.0082464
X-RAY DIFFRACTIONf_dihedral_angle_d13.254901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.330.3359900.33653226X-RAY DIFFRACTION59.73
1.33-1.360.33941100.30333947X-RAY DIFFRACTION73.35
1.36-1.40.31321330.26854748X-RAY DIFFRACTION87.68
1.4-1.450.24621490.23355325X-RAY DIFFRACTION99.06
1.45-1.50.23231520.20475427X-RAY DIFFRACTION99.96
1.5-1.560.21661500.19055383X-RAY DIFFRACTION99.95
1.56-1.630.18591520.17265425X-RAY DIFFRACTION99.96
1.63-1.720.17091500.17065383X-RAY DIFFRACTION100
1.72-1.820.18971510.1715430X-RAY DIFFRACTION100
1.82-1.970.1931520.16655398X-RAY DIFFRACTION99.96
1.97-2.160.18141510.1635432X-RAY DIFFRACTION99.98
2.16-2.480.17851510.16225439X-RAY DIFFRACTION99.96
2.48-3.120.18371540.17385476X-RAY DIFFRACTION100
3.12-29.890.17871550.16535548X-RAY DIFFRACTION99.93

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