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- PDB-9hq2: 1-Epi-Cubenol Synthase from Nonomuraea coxensis (NcECS): Open State -

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Basic information

Entry
Database: PDB / ID: 9hq2
Title1-Epi-Cubenol Synthase from Nonomuraea coxensis (NcECS): Open State
ComponentsNcECS
KeywordsLYASE / Biosynthesis / Terpenes / Type I Cyclase / Isomerization / Carbocation Chemistry / Catalysis
Biological speciesNonomuraea coxensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7555
Polymers37,5521
Non-polymers2034
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-6 kcal/mol
Surface area14780 Å2
Unit cell
Length a, b, c (Å)133.460, 133.460, 93.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-402-

MG

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Components

#1: Protein NcECS


Mass: 37552.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonomuraea coxensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine, 20%; 5 mM MgCl2; 20% PEG6000

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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: 1.8→30 Å / Num. obs: 45866 / % possible obs: 99.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6763

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.345 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18533 2293 5 %RANDOM
Rwork0.15754 ---
obs0.15894 43563 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 12 242 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132635
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142446
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.643590
X-RAY DIFFRACTIONr_angle_other_deg1.3351.585606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6075319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44120.253158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46915407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0881528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
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_it1.3863.0511276
X-RAY DIFFRACTIONr_mcbond_other1.3843.0481275
X-RAY DIFFRACTIONr_mcangle_it1.8654.5681592
X-RAY DIFFRACTIONr_mcangle_other1.8654.5711593
X-RAY DIFFRACTIONr_scbond_it1.5923.391358
X-RAY DIFFRACTIONr_scbond_other1.5923.3921359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0374.9521998
X-RAY DIFFRACTIONr_long_range_B_refined2.98558.4511456
X-RAY DIFFRACTIONr_long_range_B_other2.80757.88211220
X-RAY DIFFRACTIONr_rigid_bond_restr0.61535078
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 166 -
Rwork0.291 3157 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: -31.8043 Å / Origin y: 41.0062 Å / Origin z: 23.1564 Å
111213212223313233
T0.0648 Å2-0.0075 Å20.0059 Å2-0.0286 Å20.0002 Å2--0.0035 Å2
L0.2024 °20.1783 °2-0.2061 °2-0.5373 °2-0.1881 °2--0.628 °2
S0.0106 Å °0.0116 Å °0.0068 Å °0.0127 Å °-0.0194 Å °-0.0251 Å °0.149 Å °-0.0003 Å °0.0088 Å °

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