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- PDB-9rrz: Sesterterpene Synthase from Kitasatospora viridis (apo) -

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Basic information

Entry
Database: PDB / ID: 9rrz
TitleSesterterpene Synthase from Kitasatospora viridis (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: 1.45 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

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Assembly

Deposited unit
A: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0564
Polymers39,8081
Non-polymers2483
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint5 kcal/mol
Surface area15100 Å2
Unit cell
Length a, b, c (Å)95.640, 95.640, 114.590
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: 39807.844 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 426 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.9 M Sodium malonate

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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: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 90199 / % possible obs: 95.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.7
Reflection shellResolution: 1.45→1.55 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 16548 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.743 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17783 4508 5 %RANDOM
Rwork0.15533 ---
obs0.15646 85649 95.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å20 Å2
2---0.43 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 14 432 3141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152615
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.6373874
X-RAY DIFFRACTIONr_angle_other_deg1.2751.5695996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7225348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32320.759158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71815418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8721525
X-RAY DIFFRACTIONr_chiral_restr0.0620.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
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_it0.7662.051374
X-RAY DIFFRACTIONr_mcbond_other0.7662.0491373
X-RAY DIFFRACTIONr_mcangle_it1.063.0691719
X-RAY DIFFRACTIONr_mcangle_other1.0593.071720
X-RAY DIFFRACTIONr_scbond_it0.8272.271455
X-RAY DIFFRACTIONr_scbond_other0.8272.2711456
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0843.3322153
X-RAY DIFFRACTIONr_long_range_B_refined2.65826.3513540
X-RAY DIFFRACTIONr_long_range_B_other2.06525.0473410
X-RAY DIFFRACTIONr_rigid_bond_restr0.42235444
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 338 -
Rwork0.279 6420 -
obs--98.4 %

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