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- PDB-9wf7: Guaiadiene synthase complexed with farnesyl S-thiolodiphosphate -

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Basic information

Entry
Database: PDB / ID: 9wf7
TitleGuaiadiene synthase complexed with farnesyl S-thiolodiphosphate
ComponentsInactive (1R,4R,5S)-(-)-guaia-6,10(14)-diene synthase
KeywordsLYASE / Guaiadiene biosynthesis / Sesquiterpene cyclase / STC5 / Terpene synthase
Function / homologyTerpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / isoprenoid biosynthetic process / Isoprenoid synthase domain superfamily / metal ion binding / Chem-FPS / Inactive (1R,4R,5S)-(-)-guaia-6,10(14)-diene synthase
Function and homology information
Biological speciesGibberella fujikuroi (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsKunthic, T. / Xiang, Z.
Funding support2items
OrganizationGrant numberCountry
Other government
Other government
CitationJournal: To Be Published
Title: Structure-guided engineering of guaiadiene synthase and cytochrome P450BM3 for target- and diversity-oriented synthesis of guaiane sesquiterpenoids
Authors: Xiao, W. / Kunthic, T. / Xiang, Z.
History
DepositionAug 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inactive (1R,4R,5S)-(-)-guaia-6,10(14)-diene synthase
B: Inactive (1R,4R,5S)-(-)-guaia-6,10(14)-diene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,24010
Polymers94,2002
Non-polymers1,0408
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-63 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.881, 159.881, 159.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Inactive (1R,4R,5S)-(-)-guaia-6,10(14)-diene synthase


Mass: 47099.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) (fungus)
Gene: STC5, FFUJ_11739 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S0ENM8
#2: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Tris-HCl pH 7.5, 0.2 M LiCl, 14% (w/v) PEG 6,000, 5% (v/v) glycerol, 15% (w/v) sucrose, and 25% (w/v) hexammine cobalt (III)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.5→22.84 Å / Num. obs: 46661 / % possible obs: 98.9 % / Redundancy: 3.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.078 / Rrim(I) all: 0.158 / Χ2: 0.92 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.395 / Num. unique obs: 4596 / CC1/2: 0.899 / Rpim(I) all: 0.221 / Rrim(I) all: 0.455 / Χ2: 0.67

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: 000)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.501→22.84 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 2340 5.05 %
Rwork0.1915 --
obs0.1937 46293 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→22.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 61 468 6110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075776
X-RAY DIFFRACTIONf_angle_d0.837833
X-RAY DIFFRACTIONf_dihedral_angle_d23.3812119
X-RAY DIFFRACTIONf_chiral_restr0.042819
X-RAY DIFFRACTIONf_plane_restr0.0051010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.55160.29691140.23862565X-RAY DIFFRACTION99
2.5516-2.6070.27941420.24872586X-RAY DIFFRACTION99
2.607-2.66750.29931280.24912602X-RAY DIFFRACTION98
2.6675-2.73410.31281380.23492556X-RAY DIFFRACTION99
2.7341-2.80790.29081460.23552569X-RAY DIFFRACTION99
2.8079-2.89040.29391270.22612601X-RAY DIFFRACTION99
2.8904-2.98350.2911160.2392587X-RAY DIFFRACTION98
2.9835-3.08990.24811530.21792561X-RAY DIFFRACTION99
3.0899-3.21330.24831270.21572612X-RAY DIFFRACTION99
3.2133-3.35910.25351700.21222561X-RAY DIFFRACTION99
3.3591-3.53560.27571360.18622641X-RAY DIFFRACTION99
3.5356-3.75620.23851370.17432581X-RAY DIFFRACTION99
3.7562-4.04470.19241490.17232588X-RAY DIFFRACTION98
4.0447-4.4490.18481520.15312579X-RAY DIFFRACTION98
4.449-5.08660.18991360.15472595X-RAY DIFFRACTION98
5.0866-6.38530.211420.18412620X-RAY DIFFRACTION97
6.3853-22.840.20761270.16572549X-RAY DIFFRACTION92

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