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- PDB-9mhs: Drimenol synthase -

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Basic information

Entry
Database: PDB / ID: 9mhs
TitleDrimenol synthase
ComponentsDrimenol Synthase
KeywordsLYASE / terpene synthase / phosphatase / isoprenoid
Function / homologyN-benzyl-N,N-diethylethanaminium / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Function and homology information
Biological speciesAquimarina spongiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsOsika, K.R. / Gaynes, 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: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Crystal structure and catalytic mechanism of drimenol synthase, an unusual bifunctional terpene cyclase-phosphatase.
Authors: Osika, K.R. / Gaynes, M.N. / Christianson, D.W.
History
DepositionDec 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Drimenol Synthase
A: Drimenol Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,97514
Polymers121,7852
Non-polymers1,19012
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-50 kcal/mol
Surface area36830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.902, 76.253, 106.429
Angle α, β, γ (deg.)90.00, 111.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Drimenol Synthase


Mass: 60892.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquimarina spongiae (bacteria) / Gene: SAMN04488508_102320 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 209 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 13 mg/mL Drimenol Synthase, Tris-HCl, NaCl, TCEP, glycerol, benzyltriethylammonium chloride (BTAC), sodium pyrophosphate, Magnesium chloride hexhydrate, HEPES, sodium chloride, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.23→34.42 Å / Num. obs: 65482 / % possible obs: 99.84 % / Redundancy: 4.5 % / Biso Wilson estimate: 31.18 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.095 / Rrim(I) all: 0.199 / Net I/σ(I): 2.23
Reflection shellResolution: 2.23→2.267 Å / Rmerge(I) obs: 1.297 / Num. unique obs: 3278 / CC1/2: 0.33 / Rpim(I) all: 0.698 / Rrim(I) all: 1.477 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→34.23 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 2000 3.05 %
Rwork0.2058 --
obs0.2071 65377 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7606 0 77 197 7880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077845
X-RAY DIFFRACTIONf_angle_d0.84610677
X-RAY DIFFRACTIONf_dihedral_angle_d15.682737
X-RAY DIFFRACTIONf_chiral_restr0.0511232
X-RAY DIFFRACTIONf_plane_restr0.0071362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.280.34711410.29264465X-RAY DIFFRACTION99
2.28-2.350.26951420.27044520X-RAY DIFFRACTION100
2.35-2.420.31911400.2524462X-RAY DIFFRACTION100
2.42-2.490.33251430.24144525X-RAY DIFFRACTION100
2.49-2.580.29691420.23424513X-RAY DIFFRACTION100
2.58-2.690.26771420.22814515X-RAY DIFFRACTION100
2.69-2.810.30721440.21874550X-RAY DIFFRACTION100
2.81-2.960.27481420.21274514X-RAY DIFFRACTION100
2.96-3.140.25571430.21264523X-RAY DIFFRACTION100
3.14-3.380.25641420.19264545X-RAY DIFFRACTION100
3.38-3.720.21811430.18664535X-RAY DIFFRACTION100
3.72-4.260.23131450.17584567X-RAY DIFFRACTION100
4.26-5.370.21191440.17884588X-RAY DIFFRACTION100
5.37-34.230.21011470.20284660X-RAY DIFFRACTION100

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