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

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Basic information

Entry
Database: PDB / ID: 9hqi
TitleT-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with 2,3-DHFPP [P4(3)2(1)2(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
Chem-3E9 / (R,R)-2,3-BUTANEDIOL / (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 16, 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)73,27921
Polymers71,5112
Non-polymers1,76819
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-20 kcal/mol
Surface area24320 Å2
Unit cell
Length a, b, c (Å)131.810, 131.810, 128.430
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-984-

HOH

21B-1012-

HOH

31B-1022-

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

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Non-polymers , 6 types, 331 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-3E9 / (3S,6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl trihydrogen diphosphate


Mass: 384.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, 0.05 mM 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: 2.1→30 Å / Num. obs: 64130 / % possible obs: 96.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 8347 / Rrim(I) all: 0.595 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
PROCORdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.291 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20136 3206 5 %RANDOM
Rwork0.17044 ---
obs0.17206 60902 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.143 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4939 0 110 312 5361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135160
X-RAY DIFFRACTIONr_bond_other_d0.0010.0144849
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.6497000
X-RAY DIFFRACTIONr_angle_other_deg1.1531.57611019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4315608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59719.849332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4021560
X-RAY DIFFRACTIONr_chiral_restr0.050.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021359
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_it2.163.7862438
X-RAY DIFFRACTIONr_mcbond_other2.163.7852437
X-RAY DIFFRACTIONr_mcangle_it3.0465.6743041
X-RAY DIFFRACTIONr_mcangle_other3.0455.6753042
X-RAY DIFFRACTIONr_scbond_it2.3174.1552722
X-RAY DIFFRACTIONr_scbond_other2.3174.1562723
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1096.0873959
X-RAY DIFFRACTIONr_long_range_B_refined4.19744.6126044
X-RAY DIFFRACTIONr_long_range_B_other4.04644.2845964
X-RAY DIFFRACTIONr_rigid_bond_restr0.688310009
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 238 -
Rwork0.251 4513 -
obs--98.81 %
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)
10.8963-0.03170.30660.49340.03930.57060.00390.0013-0.025-0.02-0.0226-0.0618-0.01660.0070.01860.0124-0.0036-0.01530.02120.01280.03635.78-40.98211.8652
21.33650.1395-0.1360.72270.16640.5395-0.0014-0.204-0.02030.09790.06540.0189-0.0146-0.0098-0.06390.03320.03140.0020.06110.00730.0143-22.7813-28.012524.0339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 993
2X-RAY DIFFRACTION2B4 - 993

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