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- PDB-9rp0: Ensemble refined structure of CotB2 in complex with 2-fluoro-3,7,... -

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Basic information

Entry
Database: PDB / ID: 9rp0
TitleEnsemble refined structure of CotB2 in complex with 2-fluoro-3,7,18-dolabellatriene
ComponentsCyclooctat-9-en-7-ol synthase
KeywordsHYDROLASE / TERPENE SYNTHASE / CYCLOOCTATIN / DITERPENCE SYNTHASE
Function / homology
Function and homology information


cyclooctat-9-en-7-ol synthase / isomerase activity / lyase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
ACETONITRILE / 2-fluoro-3,7,18-dolabellatriene / : / PYROPHOSPHATE / Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHelmer, C.P.O. / Loll, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
German-Israeli Foundation for Research and DevelopmentI-85-302.14-2018 Germany
German Research Foundation (DFG)RTG 2473-1 Germany
Citation
Journal: Protein Sci. / Year: 2025
Title: The initial dynamics of product release in terpene synthases-The case of CotB2.
Authors: Gupta, P.K. / Helmer, C.P.O. / Ringel, M. / Loll, B. / Bruck, T. / Major, D.T.
#1: Journal: Nat Common / Year: 2018
Title: Towards a comprehensive understanding of the structural dynamics of a bacterial diterpene synthase during catalysis.
Authors: Driller, R. / Janke, S. / Fuchs, M. / Warner, E. / Mhashal, A.R. / Major, D.T. / Christmann, M. / Brueck, T. / Loll, B.
History
DepositionJun 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclooctat-9-en-7-ol synthase
B: Cyclooctat-9-en-7-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,98825
Polymers73,5412
Non-polymers2,44723
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.885, 98.722, 105.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Number of models50

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cyclooctat-9-en-7-ol synthase


Mass: 36770.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria)
Gene: CotB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase

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Non-polymers , 9 types, 240 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical ChemComp-EXW / 2-fluoro-3,7,18-dolabellatriene


Mass: 290.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31F
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#8: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) polyethylene glycol 400, 100 mM HEPES at pH 7.5 and 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→47.42 Å / Num. obs: 61262 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.65 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.114 / Num. unique obs: 3769 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.42 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.95
RfactorNum. reflection% reflection
Rfree0.195 2097 3.43 %
Rwork0.1653 --
obs0.1663 61143 99.45 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4847 0 107 217 5171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.348
X-RAY DIFFRACTIONf_dihedral_angle_d18.07
X-RAY DIFFRACTIONf_chiral_restr0.078
X-RAY DIFFRACTIONf_plane_restr0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.27341340.27833769X-RAY DIFFRACTION97
1.84-1.890.33471380.25333903X-RAY DIFFRACTION99
1.89-1.940.27851360.2323854X-RAY DIFFRACTION99
1.94-20.2951390.20833913X-RAY DIFFRACTION100
2-2.060.28621380.18673880X-RAY DIFFRACTION99
2.06-2.140.20631390.18273905X-RAY DIFFRACTION100
2.14-2.220.22351400.16183919X-RAY DIFFRACTION100
2.22-2.320.20331400.15543952X-RAY DIFFRACTION100
2.32-2.450.16791390.14983895X-RAY DIFFRACTION100
2.45-2.60.18791400.15093962X-RAY DIFFRACTION100
2.6-2.80.18321400.14863940X-RAY DIFFRACTION100
2.8-3.080.15891410.14563975X-RAY DIFFRACTION100
3.08-3.530.17411420.14363992X-RAY DIFFRACTION100
3.53-4.440.15761430.14254013X-RAY DIFFRACTION100
4.45-47.420.18491480.17734174X-RAY DIFFRACTION99

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