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- PDB-9hqb: 1-Epi-Cubenol Synthase from Nonomuraea coxensis (NcECS) in comple... -

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Basic information

Entry
Database: PDB / ID: 9hqb
Title1-Epi-Cubenol Synthase from Nonomuraea coxensis (NcECS) in complex with 2,3-DHFPP
ComponentsNcECS
KeywordsLYASE / Biosynthesis / Terpenes / Type I Cyclase / Isomerization / Carbocation Chemistry / Catalysis
Function / homologyChem-3E9 / (R,R)-2,3-BUTANEDIOL
Function and homology information
Biological speciesNonomuraea coxensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: NcECS
B: NcECS
C: NcECS
D: NcECS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,80620
Polymers150,2094
Non-polymers1,59716
Water9,494527
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-124 kcal/mol
Surface area45460 Å2
Unit cell
Length a, b, c (Å)70.780, 87.590, 102.010
Angle α, β, γ (deg.)90.00, 106.76, 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
NcECS


Mass: 37552.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonomuraea coxensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 543 molecules

#2: Chemical ChemComp-3E9 / (3S,6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl trihydrogen diphosphate


Mass: 384.342 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H30O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES; 0.05 M MgCl2; 12% PEG 20000

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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 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 99381 / % possible obs: 97.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14639

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.646 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19226 4967 5 %RANDOM
Rwork0.1549 ---
obs0.15687 94391 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.349 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å2-0 Å2-0.97 Å2
2--0.25 Å2-0 Å2
3---3.06 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9927 0 95 527 10549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01310277
X-RAY DIFFRACTIONr_bond_other_d0.0010.0149536
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.64114016
X-RAY DIFFRACTIONr_angle_other_deg1.2541.57921842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.89951232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10120.146618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.667151577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.10215107
X-RAY DIFFRACTIONr_chiral_restr0.060.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022498
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_it1.632.564955
X-RAY DIFFRACTIONr_mcbond_other1.6292.5594954
X-RAY DIFFRACTIONr_mcangle_it2.1833.8336178
X-RAY DIFFRACTIONr_mcangle_other2.1833.8346179
X-RAY DIFFRACTIONr_scbond_it1.7062.8495322
X-RAY DIFFRACTIONr_scbond_other1.7062.855323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2324.1697839
X-RAY DIFFRACTIONr_long_range_B_refined3.22848.63845005
X-RAY DIFFRACTIONr_long_range_B_other3.13748.53144648
X-RAY DIFFRACTIONr_rigid_bond_restr0.74319813
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 369 -
Rwork0.258 7029 -
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)
10.1858-0.1624-0.02540.2562-0.01120.1458-0.0275-0.0287-0.0127-0.02240.02550.0007-0.00640.01840.00190.03-0.00480.0090.04880.01720.018634.73743.487737.1876
20.2511-0.0143-0.04480.15350.0230.1368-0.022-0.0082-0.0319-0.00540.00650.0249-0.0190.00960.01550.0283-0.00670.0110.04940.01180.01592.06026.768739.9225
30.08610.060.00360.2730.14660.1179-0.0278-0.0206-0.0034-0.02640.02050.005-0.03950.04770.00740.0574-0.02050.00020.04150.00760.00228.14846.573113.7503
40.21190.1453-0.03320.1762-0.02390.2051-0.0447-0.0310.0194-0.06980.02830.03880.0150.00050.01640.0717-0.0203-0.01560.03620.01310.01216.648227.806-0.6513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 903
2X-RAY DIFFRACTION2B12 - 903
3X-RAY DIFFRACTION3C2 - 903
4X-RAY DIFFRACTION4D15 - 314

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