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- PDB-9rs2: Sesterterpene Synthase from Kitasatospora viridis in complex with... -

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Basic information

Entry
Database: PDB / ID: 9rs2
TitleSesterterpene Synthase from Kitasatospora viridis in complex with the surrogate GFSPP
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: 2.3 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
Revision 1.1Oct 8, 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

Downloads & links

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Assembly

Deposited unit
A: Terpene synthase
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,01717
Polymers79,6162
Non-polymers1,40115
Water1,38777
1
A: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6238
Polymers39,8081
Non-polymers8157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3949
Polymers39,8081
Non-polymers5878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.190, 97.190, 70.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11B-540-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Terpene synthase


Mass: 39807.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora viridis (bacteria) / Gene: FHX73_1760 / Plasmid: pETDuet-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A561SAF2, Lyases; Carbon-oxygen lyases; Acting on phosphates

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Non-polymers , 6 types, 92 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1JI6 / [(2~{E},6~{E},10~{E},14~{E})-3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaenyl]sulfanyl-phosphonooxy-phosphinic acid


Mass: 534.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H44O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M PCB buffer, 25% w/v PEG 1500

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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: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 28407 / % possible obs: 96 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3389 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 22.376 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23801 1420 5 %RANDOM
Rwork0.19259 ---
obs0.19485 26978 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5404 0 88 77 5569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135635
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155236
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.6467681
X-RAY DIFFRACTIONr_angle_other_deg1.0451.58311991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5635672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.84620.629318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66515829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2971552
X-RAY DIFFRACTIONr_chiral_restr0.040.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026323
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021379
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_it0.9913.9872706
X-RAY DIFFRACTIONr_mcbond_other0.9843.9862705
X-RAY DIFFRACTIONr_mcangle_it1.4495.9693372
X-RAY DIFFRACTIONr_mcangle_other1.4495.973373
X-RAY DIFFRACTIONr_scbond_it0.8124.1332929
X-RAY DIFFRACTIONr_scbond_other0.8114.1332930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2176.1454310
X-RAY DIFFRACTIONr_long_range_B_refined2.3445.936408
X-RAY DIFFRACTIONr_long_range_B_other2.26745.9116402
X-RAY DIFFRACTIONr_rigid_bond_restr0.218310871
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 106 -
Rwork0.305 2011 -
obs--97.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43640.00270.03110.268-0.07240.3439-0.0019-0.01750.0121-0.0326-0.0186-0.04070.02880.07180.02050.030.00060.01640.06550.01470.015337.7918-24.0615-5.2032
20.27410.04610.0040.0874-0.00870.14840.0076-0.00810.0178-0.00660.00040.01010.0061-0.0017-0.00790.06220.00260.00240.05350.00170.00235.003-26.1680.1137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 904
2X-RAY DIFFRACTION2B5 - 354

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