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- PDB-9y6m: Avermitilol synthase: Complex with Mg, inorganic pyrophosphate, a... -

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Basic information

Entry
Database: PDB / ID: 9y6m
TitleAvermitilol synthase: Complex with Mg, inorganic pyrophosphate, and adamantane 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 / : / 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

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Assembly

Deposited unit
A: Avermitilol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4048
Polymers36,8391
Non-polymers5657
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.552, 56.250, 72.766
Angle α, β, γ (deg.)90.000, 125.300, 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: 36838.605 Da / Num. of mol.: 1
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, 193 molecules

#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#3: Chemical ChemComp-A1CSW / 1-(trimethyl-$l^{4}-azanyl)adamantane


Mass: 194.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H24N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / 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.: 186 / 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: 43.22 %
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→29.94 Å / Num. obs: 57615 / % possible obs: 96.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 13.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.051 / Net I/σ(I): 7.9
Reflection shellResolution: 1.42→1.44 Å / Rmerge(I) obs: 1.142 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2971 / CC1/2: 0.457 / Rpim(I) all: 0.628

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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→29.94 Å / SU ML: 0.1756 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 2000 3.47 %
Rwork0.1598 55574 -
obs0.1613 57574 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.85 Å2
Refinement stepCycle: LAST / Resolution: 1.42→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 34 186 2750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472628
X-RAY DIFFRACTIONf_angle_d0.77333589
X-RAY DIFFRACTIONf_chiral_restr0.0655384
X-RAY DIFFRACTIONf_plane_restr0.008474
X-RAY DIFFRACTIONf_dihedral_angle_d11.7768928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.3581470.30474080X-RAY DIFFRACTION99.6
1.45-1.490.29111370.25153803X-RAY DIFFRACTION92.77
1.49-1.540.27411370.22433819X-RAY DIFFRACTION92.67
1.54-1.590.25941470.19154087X-RAY DIFFRACTION100
1.59-1.640.23241470.17224076X-RAY DIFFRACTION99.88
1.64-1.710.18741480.15684100X-RAY DIFFRACTION100
1.71-1.790.21531490.14924135X-RAY DIFFRACTION100
1.79-1.880.19871460.13864059X-RAY DIFFRACTION99.22
1.88-20.19751220.14253405X-RAY DIFFRACTION82.68
2-2.150.18551360.1443760X-RAY DIFFRACTION91.48
2.15-2.370.17841410.14493923X-RAY DIFFRACTION95.31
2.37-2.710.18621450.15124053X-RAY DIFFRACTION98.04
2.71-3.420.20731500.15954142X-RAY DIFFRACTION100
3.42-29.940.16711480.14524132X-RAY DIFFRACTION97.49

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