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- PDB-9rs5: Sesterterpene Synthase from Kitasatospora viridis (I303Y-Variant, apo) -

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Basic information

Entry
Database: PDB / ID: 9rs5
TitleSesterterpene Synthase from Kitasatospora viridis (I303Y-Variant, apo)
ComponentsTerpene synthase
KeywordsLYASE / Type I Terpene Synthases / Terpene Cyclization Mechanism / Carbocation Cascade / Enzyme Engineering / Active Site Mutagenesis / Chemodiversity
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / metal ion binding / Terpene synthase
Function and homology information
Biological speciesKitasatospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLi, H. / Troycke, P. / Yin, Z. / Groll, M. / Dickschat, J.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 (project number 542938137) Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structure-Guided Engineering of a Bacterial Sesterterpene Synthase for Sesterviridene Diversification.
Authors: Li, H. / Troycke, P. / Yin, Z. / Groll, M. / Dickschat, J.S.
History
DepositionJun 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0372
Polymers39,9451
Non-polymers921
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-1 kcal/mol
Surface area14780 Å2
Unit cell
Length a, b, c (Å)95.530, 95.530, 114.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Terpene synthase


Mass: 39944.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora viridis (bacteria) / Gene: FHX73_1760 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A561SAF2, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 1.4 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 63976 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.2
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 10189 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.966 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 3198 5 %RANDOM
Rwork0.15687 ---
obs0.15799 60770 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 6 354 3055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132863
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152627
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.6373924
X-RAY DIFFRACTIONr_angle_other_deg1.221.576030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9485353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22720.813160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99815424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5781525
X-RAY DIFFRACTIONr_chiral_restr0.0570.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02710
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7932.2071397
X-RAY DIFFRACTIONr_mcbond_other0.7932.2061396
X-RAY DIFFRACTIONr_mcangle_it1.1383.3011755
X-RAY DIFFRACTIONr_mcangle_other1.1373.3021756
X-RAY DIFFRACTIONr_scbond_it0.7632.3981466
X-RAY DIFFRACTIONr_scbond_other0.7632.3991467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0763.5392170
X-RAY DIFFRACTIONr_long_range_B_refined2.40327.7453607
X-RAY DIFFRACTIONr_long_range_B_other2.08226.8293494
X-RAY DIFFRACTIONr_rigid_bond_restr0.33935490
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 232 -
Rwork0.237 4409 -
obs--99.85 %

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