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- PDB-9y6k: Avermitilol synthase T215V: Complex with Mg, inorganic pyrophosph... -

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Basic information

Entry
Database: PDB / ID: 9y6k
TitleAvermitilol synthase T215V: 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: 1.42 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)37,4008
Polymers36,8371
Non-polymers5637
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.373, 56.503, 72.557
Angle α, β, γ (deg.)90.000, 125.150, 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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Avermitilol synthase


Mass: 36836.633 Da / Num. of mol.: 1 / Mutation: T215V
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, 214 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#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-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#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.: 207 / 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: 2.17 Å3/Da / Density % sol: 43.31 %
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: 1.42→31.46 Å / Num. obs: 59408 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.052 / Net I/σ(I): 8.5
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 1.053 / Num. unique obs: 2890 / CC1/2: 0.344 / Rpim(I) all: 0.736

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→31.46 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 2972 5.04 %
Rwork0.1844 55946 -
obs0.1853 58918 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.43 Å2
Refinement stepCycle: LAST / Resolution: 1.42→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 34 207 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512620
X-RAY DIFFRACTIONf_angle_d0.8313566
X-RAY DIFFRACTIONf_chiral_restr0.0663377
X-RAY DIFFRACTIONf_plane_restr0.0094472
X-RAY DIFFRACTIONf_dihedral_angle_d13.4552928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.31141280.3072353X-RAY DIFFRACTION87.58
1.44-1.470.31261590.29392495X-RAY DIFFRACTION94.25
1.47-1.490.27461440.2652637X-RAY DIFFRACTION97.85
1.49-1.520.29211600.24822619X-RAY DIFFRACTION99.21
1.52-1.550.24231480.24032646X-RAY DIFFRACTION99.32
1.55-1.590.23261190.22882721X-RAY DIFFRACTION99.54
1.59-1.620.25861300.2132667X-RAY DIFFRACTION99.43
1.62-1.660.23331480.21152680X-RAY DIFFRACTION99.61
1.66-1.710.21811470.19962669X-RAY DIFFRACTION99.33
1.71-1.760.23871360.19722661X-RAY DIFFRACTION99.4
1.76-1.820.21131110.18622741X-RAY DIFFRACTION99.51
1.82-1.880.18931500.18392686X-RAY DIFFRACTION99.65
1.88-1.960.21991310.18342693X-RAY DIFFRACTION99.72
1.96-2.050.18521230.18112706X-RAY DIFFRACTION99.54
2.05-2.150.21441380.17612685X-RAY DIFFRACTION99.75
2.15-2.290.19171380.16732689X-RAY DIFFRACTION99.23
2.29-2.470.19221570.1692674X-RAY DIFFRACTION99.51
2.47-2.710.16651610.17592687X-RAY DIFFRACTION99.72
2.71-3.110.20721470.1832723X-RAY DIFFRACTION100
3.11-3.910.18181560.16782721X-RAY DIFFRACTION100
3.91-31.460.1621410.15622793X-RAY DIFFRACTION99.86

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