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

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Basic information

Entry
Database: PDB / ID: 9hqz
TitleT-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with converted 1,2-DHNPP (compound 1)
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 / FARNESYL / 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 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)72,32312
Polymers71,5112
Non-polymers81210
Water2,378132
1
A: (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3638
Polymers35,7561
Non-polymers6077
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9604
Polymers35,7561
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.990, 75.310, 132.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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(DE3) (bacteria) / References: UniProt: A7NH01, (+)-T-muurolol synthase

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Non-polymers , 6 types, 142 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES; 0.05 M MgCl2; 25% PEG 1000

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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: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 40308 / % possible obs: 97.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5461 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.947 / SU B: 14.866 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22551 2015 5 %RANDOM
Rwork0.16359 ---
obs0.16665 38279 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.583 Å2
Baniso -1Baniso -2Baniso -3
1-8.55 Å20 Å2-0 Å2
2---4.44 Å20 Å2
3----4.12 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 50 132 5018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134996
X-RAY DIFFRACTIONr_bond_other_d0.0080.0154661
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.6446789
X-RAY DIFFRACTIONr_angle_other_deg1.2911.58510592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0675592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34220.188319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25415775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7261556
X-RAY DIFFRACTIONr_chiral_restr0.0540.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021324
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_it4.8124.7412383
X-RAY DIFFRACTIONr_mcbond_other4.8124.742382
X-RAY DIFFRACTIONr_mcangle_it5.7947.1142970
X-RAY DIFFRACTIONr_mcangle_other5.7937.1152971
X-RAY DIFFRACTIONr_scbond_it5.4745.0612613
X-RAY DIFFRACTIONr_scbond_other5.4745.0622614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5957.4633820
X-RAY DIFFRACTIONr_long_range_B_refined6.85555.5365832
X-RAY DIFFRACTIONr_long_range_B_other6.82855.4735816
X-RAY DIFFRACTIONr_rigid_bond_restr3.86939657
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 148 -
Rwork0.369 2808 -
obs--99.19 %
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)
10.0242-0.02260.01720.0407-0.00470.0463-0.00180.00610.0021-0.0041-0.00110.00320.00140.00380.00290.0028-0.00180.00010.01450.00190.01796.49752.13550.4082
20.0142-0.00010.02830.00240.00360.1338-0.004-0.0073-0.00870.0030.00350.0006-0.0307-0.00780.00050.01640.00120.00150.0125-0.00060.015210.98897.5475-36.3443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 993
2X-RAY DIFFRACTION2B4 - 801

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