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- PDB-29mt: Sesterterpene Synthase from Streptomyces mobaraensis (Sestermobar... -

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Basic information

Entry
Database: PDB / ID: 29mt
TitleSesterterpene Synthase from Streptomyces mobaraensis (Sestermobaraene Synthase, SmTS1, apo)
ComponentsGlutamate dehydrogenase/leucine dehydrogenase
KeywordsLYASE / Type I Terpene Synthases / Terpene Cyclization Mechanism / Carbocation Cascade / Enzyme Engineering / Active Site Mutagenesis / Chemodiversity
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Glutamate dehydrogenase/leucine dehydrogenase
Function and homology information
Biological speciesStreptomyces mobaraensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Glutamate dehydrogenase/leucine dehydrogenase
B: Glutamate dehydrogenase/leucine dehydrogenase
C: Glutamate dehydrogenase/leucine dehydrogenase
D: Glutamate dehydrogenase/leucine dehydrogenase
E: Glutamate dehydrogenase/leucine dehydrogenase
F: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,78212
Polymers237,3276
Non-polymers4556
Water18,8081044
1
A: Glutamate dehydrogenase/leucine dehydrogenase
B: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2313
Polymers79,1092
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-9 kcal/mol
Surface area25690 Å2
MethodPISA
2
F: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules

C: Glutamate dehydrogenase/leucine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)79,2875
Polymers79,1092
Non-polymers1783
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4210 Å2
ΔGint-18 kcal/mol
Surface area25850 Å2
MethodPISA
3
E: Glutamate dehydrogenase/leucine dehydrogenase
hetero molecules

D: Glutamate dehydrogenase/leucine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)79,2634
Polymers79,1092
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_666x+1,y+1,z+11
Buried area4360 Å2
ΔGint-8 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.820, 81.560, 98.720
Angle α, β, γ (deg.)101.63, 97.98, 93.90
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glutamate dehydrogenase/leucine dehydrogenase


Mass: 39554.457 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Gene: H340_07296 / Plasmid: pETDuet-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M3CB08

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Non-polymers , 5 types, 1050 molecules

#2: 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
#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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1044 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Mes, 0.2 M MgCl2, 10% PEG 4000

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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: Sep 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 235171 / % possible obs: 94.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.743 / Num. unique obs: 37502 / % possible all: 96

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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: 1.7→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.567 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20242 11757 5 %RANDOM
Rwork0.16211 ---
obs0.16412 223391 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.332 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.95 Å20.25 Å2
2---0.36 Å2-0.9 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15357 0 29 1044 16430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01315970
X-RAY DIFFRACTIONr_bond_other_d0.0010.01414664
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.64921874
X-RAY DIFFRACTIONr_angle_other_deg1.2451.57433639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36751948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14520.746912
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.089152328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.91215144
X-RAY DIFFRACTIONr_chiral_restr0.0610.22079
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023839
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_it1.6032.4257820
X-RAY DIFFRACTIONr_mcbond_other1.6022.4247819
X-RAY DIFFRACTIONr_mcangle_it2.1493.6289758
X-RAY DIFFRACTIONr_mcangle_other2.1493.6289759
X-RAY DIFFRACTIONr_scbond_it1.7212.7358150
X-RAY DIFFRACTIONr_scbond_other1.7212.7358151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2543.99612117
X-RAY DIFFRACTIONr_long_range_B_refined3.09629.61118753
X-RAY DIFFRACTIONr_long_range_B_other2.90929.34518526
X-RAY DIFFRACTIONr_rigid_bond_restr0.778330634
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 877 -
Rwork0.264 16667 -
obs--96.3 %
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)
10.1671-0.0496-0.06230.11050.02960.0496-0.00030.0068-0.010.0022-0.00510.00380.00620.00180.00550.0146-0.0044-0.00270.00580.00620.012466.080854.6729-23.8475
20.1575-0.0267-0.0060.10350.01820.07060.00550.01360.02320.0067-0.01020.01940.00340.00350.00470.0119-0.0040.00250.00570.00650.027244.4977.623-22.5526
30.0901-0.04610.01250.1678-0.06970.1356-0.0053-0.0064-0.01230.00460.00910.0186-0.0066-0.014-0.00380.0065-0.0043-0.00670.00650.00720.017423.845628.5922-9.6232
40.06770.01180.0250.16580.12940.2321-0.0011-0.0096-0.0024-0.01980.012-0.0088-0.00910.0044-0.01090.017-0.0068-0.00390.00740.0050.00648.878225.4692-51.9405
50.02850.00510.02140.16570.20440.32040.0008-0.0009-0.007-0.02850.0367-0.0214-0.0220.0428-0.03760.0249-0.0120.00270.0113-0.00170.010469.198669.755416.9312
60.119-0.04320.0540.1231-0.01840.1682-0.0073-0.0167-0.00960.01970.01070.003-0.0094-0.0068-0.00340.0173-0.0036-0.00580.00850.00830.008955.594643.4985-80.0384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 339
2X-RAY DIFFRACTION2B8 - 348
3X-RAY DIFFRACTION3C8 - 349
4X-RAY DIFFRACTION4D17 - 349
5X-RAY DIFFRACTION5E9 - 349
6X-RAY DIFFRACTION6F9 - 349

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