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- PDB-9mlo: Drimenol Synthase - Farnesyl Thiol Complex -

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Basic information

Entry
Database: PDB / ID: 9mlo
TitleDrimenol Synthase - Farnesyl Thiol Complex
ComponentsHaloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
KeywordsLYASE / terpene synthase / phosphatase / isoprenoid
Function / homologyHaloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily / : / PHOSPHATE ION / Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
Function and homology information
Biological speciesAquimarina spongiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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 19, 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: Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
A: Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,85110
Polymers121,7852
Non-polymers1,0658
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-33 kcal/mol
Surface area39020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.741, 154.741, 132.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED


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 (E. coli) / References: UniProt: A0A1M6CXF0

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Non-polymers , 5 types, 102 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1BMF / (2E,6E)-3,7,11-trimethyldodeca-2,6,10-triene-1-thiol


Mass: 238.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 13 mg/mL AsDMS, Tris-HCl, NaCl, TCEP, glycerol, farnesyl S-thiolodiphosphate (FSPP), Magnesium chloride hexahydrate, Sodium citrate tribasic dihydrate, Jeffamine ED-2001

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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: 0.92 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: 2.64→34.6 Å / Num. obs: 47665 / % possible obs: 99.87 % / Redundancy: 17 % / CC1/2: 0.993 / Rmerge(I) obs: 0.406 / Rpim(I) all: 0.101 / Rrim(I) all: 0.419 / Net I/σ(I): 7
Reflection shellResolution: 2.643→2.689 Å / Rmerge(I) obs: 3.92 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2337 / CC1/2: 0.339 / Rpim(I) all: 0.928 / Rrim(I) all: 3.92 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata reduction
Zanudadata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→34.6 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 2000 4.2 %
Rwork0.2166 --
obs0.2186 47665 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7552 0 68 94 7714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087785
X-RAY DIFFRACTIONf_angle_d1.01710613
X-RAY DIFFRACTIONf_dihedral_angle_d15.292673
X-RAY DIFFRACTIONf_chiral_restr0.0491237
X-RAY DIFFRACTIONf_plane_restr0.0071358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.710.34531400.30143194X-RAY DIFFRACTION100
2.71-2.780.33341400.29883185X-RAY DIFFRACTION100
2.78-2.860.3561400.29123222X-RAY DIFFRACTION100
2.86-2.960.32311420.27473220X-RAY DIFFRACTION100
2.96-3.060.32411400.27273211X-RAY DIFFRACTION100
3.06-3.180.33281410.27553242X-RAY DIFFRACTION100
3.18-3.330.30921420.2463224X-RAY DIFFRACTION100
3.33-3.510.31331430.22653255X-RAY DIFFRACTION100
3.51-3.720.27331420.20753239X-RAY DIFFRACTION100
3.72-4.010.2361420.19663263X-RAY DIFFRACTION100
4.01-4.410.24451440.16933291X-RAY DIFFRACTION100
4.42-5.050.20541450.16873279X-RAY DIFFRACTION100
5.05-6.360.24451450.21513345X-RAY DIFFRACTION100
6.36-34.60.21991540.19863495X-RAY DIFFRACTION100

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