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- PDB-9hr0: T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in comple... -

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Basic information

Entry
Database: PDB / ID: 9hr0
TitleT-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with converted 10,11-DHFPP (compound 2+)
Components(+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
KeywordsLYASE / Biosynthesis / Terpenes / Type I Cyclase / Isomerization / Carbocation Chemistry / Catalysis
Function / homology
Function and homology information


(+)-T-muurolol synthase / terpene synthase activity / terpenoid biosynthetic process / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
: / (R,R)-2,3-BUTANEDIOL / PYROPHOSPHATE 2- / (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGroll, M. / Li, H. / Troycke, P. / Dickschat, J.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Mimics of Hydrocarbon Intermediates Reveal Counterclockwise Cyclization Pathways in the Sesquiterpene Synthases TmS and NcECS.
Authors: Groll, M. / Li, H. / Troycke, P. / Kaila, V.R.I. / Dickschat, J.S.
History
DepositionDec 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
B: (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,18722
Polymers71,5112
Non-polymers1,67520
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-41 kcal/mol
Surface area24330 Å2
Unit cell
Length a, b, c (Å)132.600, 132.600, 130.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-1000-

HOH

21B-1041-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing) / Terpene cyclase / Type I terpene cyclase


Mass: 35755.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus castenholzii (bacteria) / Gene: Rcas_0622 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7NH01, (+)-T-muurolol synthase

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Non-polymers , 6 types, 402 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-A1IW0 / (2~{Z},6~{E})-3,7,11-trimethyldodeca-2,6-diene


Mass: 208.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#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.: 382 / 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: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES; 0.05 M MgCl2; 15% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 69492 / % possible obs: 95 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.7
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9292 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.9 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19642 3473 5 %RANDOM
Rwork0.14665 ---
obs0.14926 65995 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2--0.4 Å2-0 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 104 382 5435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135197
X-RAY DIFFRACTIONr_bond_other_d0.0040.0154896
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.6537055
X-RAY DIFFRACTIONr_angle_other_deg1.2931.59511125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5195617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45819.91334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56215814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7081562
X-RAY DIFFRACTIONr_chiral_restr0.0550.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021377
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_it2.8044.1892453
X-RAY DIFFRACTIONr_mcbond_other2.8034.1882452
X-RAY DIFFRACTIONr_mcangle_it3.7756.2843063
X-RAY DIFFRACTIONr_mcangle_other3.7766.2853064
X-RAY DIFFRACTIONr_scbond_it3.0874.6212744
X-RAY DIFFRACTIONr_scbond_other3.0884.6222745
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1496.7653989
X-RAY DIFFRACTIONr_long_range_B_refined5.27649.26142
X-RAY DIFFRACTIONr_long_range_B_other4.96648.8436048
X-RAY DIFFRACTIONr_rigid_bond_restr0.966310093
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 258 -
Rwork0.219 4897 -
obs--96.72 %
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)
10.05130.02060.00720.0305-0.00040.00170.0024-0.00760.00270.0107-0.00060.002-0.0011-0.0014-0.00190.00440.00080.00030.0014-0.00050.0176-23.1738-27.88824.2259
20.01730.00160.0130.0028-0.00140.0125-0.00050.0023-0.0002-0.0006-0.0004-0.00180.00020.00240.0010.00020.0001-0.00010.0005-0.00030.01795.6057-41.411912.1433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 993
2X-RAY DIFFRACTION2B4 - 993

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