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- PDB-29mv: Sesterterpene Synthase from Streptomyces subrutilus (Subrutilane ... -

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Basic information

Entry
Database: PDB / ID: 29mv
TitleSesterterpene Synthase from Streptomyces subrutilus (Subrutilane Synthase, SrS) in complex with the surrogate geranyl-farnesyl-thiopyrophosphate (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 / : / DI(HYDROXYETHYL)ETHER / Terpene synthase
Function and homology information
Biological speciesStreptomyces subrutilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTroycke, P. / Li, H. / Yang, K. / Dickschat, J.S. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 (project number 542938137) Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Local Active-Site Architecture Directs Divergent Carbocation Cascades in Sesterterpene Synthases.
Authors: Troycke, P. / Li, H. / Yang, K. / Dickschat, J.S. / Groll, M.
History
DepositionMar 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
C: Terpene synthase
D: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,26716
Polymers160,8394
Non-polymers1,42812
Water4,432246
1
A: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0157
Polymers40,2101
Non-polymers8066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)40,2101
Polymers40,2101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5284
Polymers40,2101
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5144
Polymers40,2101
Non-polymers3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.910, 89.630, 102.690
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Terpene synthase


Mass: 40209.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces subrutilus (bacteria) / Gene: CP968_31920, GCM10010371_68870 / Plasmid: pETDuet-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A5P2UZR8, Lyases; Carbon-oxygen lyases; Acting on phosphates

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Non-polymers , 5 types, 258 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 100 mM Bicine, 30% PEG 6000

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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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 57484 / % possible obs: 95 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6956 / % possible all: 96.4

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.324 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21103 2874 5 %RANDOM
Rwork0.17909 ---
obs0.18072 54591 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.51 Å2
2---0.03 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10728 0 91 246 11065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311134
X-RAY DIFFRACTIONr_bond_other_d0.0010.01410343
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.64415214
X-RAY DIFFRACTIONr_angle_other_deg1.0621.56723786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04751342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37820.522604
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2621598
X-RAY DIFFRACTIONr_chiral_restr0.0420.21469
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022575
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_it0.82.9595395
X-RAY DIFFRACTIONr_mcbond_other0.82.9595394
X-RAY DIFFRACTIONr_mcangle_it1.1584.4276725
X-RAY DIFFRACTIONr_mcangle_other1.1584.4276726
X-RAY DIFFRACTIONr_scbond_it0.6863.0655739
X-RAY DIFFRACTIONr_scbond_other0.6863.0655740
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.994.5648489
X-RAY DIFFRACTIONr_long_range_B_refined1.96334.19512596
X-RAY DIFFRACTIONr_long_range_B_other1.91234.19412547
X-RAY DIFFRACTIONr_rigid_bond_restr0.241321477
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
Rfree0.281 214 -
Rwork0.193 4049 -
obs--96.4 %
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)
10.0120.0104-0.01510.0486-0.00490.039-0.0005-0.0054-0.0003-0.0019-0.001-0.00180-0.00210.00150.00980.0001-0.00720.02250.00040.005627.7009-1.13610.4893
20.0093-0.00870.02090.0328-0.0080.0533-0.00030.00320.0015-0.0023-0.0007-0.0061-0.00150.00440.0010.0074-0.0008-0.00650.0242-0.00180.008160.7631-5.17184.2904
30.0254-0.00110.00480.041-0.00380.0230.0017-0.0004-0.0002-0.0035-0.00150.00160.0010.0034-0.00030.009-0.0008-0.00580.02120.00070.003833.3051-11.0805-40.7312
40.0386-0.03230.0060.0271-0.00540.00250.00240.0002-0.008-0.0012-0.00150.00640.00060.0057-0.00090.0089-0.0021-0.00580.02180.00180.00575.376-7.7836-47.1542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-IDLabel asym-ID
1X-RAY DIFFRACTION1A12 - 364
2X-RAY DIFFRACTION2B14 - 364
3X-RAY DIFFRACTION3C14 - 364
4X-RAY DIFFRACTION4D14 - 364
5X-RAY DIFFRACTION1E
6X-RAY DIFFRACTION3K
7X-RAY DIFFRACTION1F
8X-RAY DIFFRACTION1G
9X-RAY DIFFRACTION1H
10X-RAY DIFFRACTION1I
11X-RAY DIFFRACTION1J
12X-RAY DIFFRACTION3L
13X-RAY DIFFRACTION3M
14X-RAY DIFFRACTION4N
15X-RAY DIFFRACTION4O
16X-RAY DIFFRACTION4P

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