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- PDB-9rp2: Ensemble refined structure of CotB2 F107A in complex with alendronate -

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Basic information

Entry
Database: PDB / ID: 9rp2
TitleEnsemble refined structure of CotB2 F107A in complex with alendronate
ComponentsCyclooctat-9-en-7-ol synthase
KeywordsHYDROLASE / TERPENE SYNTHASE / CYCLOOCTATIN / DITERPENCE SYNTHASE
Function / homologycyclooctat-9-en-7-ol synthase / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / isomerase activity / lyase activity / metal ion binding / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / Cyclooctat-9-en-7-ol synthase
Function and homology information
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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: To Be Published
Title: Ensemble refined structure of CotB2 F107A in complex with alendronate
Authors: Helmer, C.P.O. / Loll, B.
#1: Journal: J Am Chem Soc / Year: 2020
Title: The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol.
Authors: Raz, K. / Driller, R. / Dimos, N. / Ringel, M. / Brueck, T. / Loll, B. / Major, D.T.
History
DepositionJun 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)74,56816
Polymers73,3892
Non-polymers1,18014
Water6,359353
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)62.811, 98.050, 106.830
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: 36694.426 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 DH5[alpha] (bacteria) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase

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Non-polymers , 5 types, 367 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-AHD / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / ALENDRONATE / FOSAMAX (TM)


Mass: 245.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris/HCl pH 8.5 9% (w/v) PEG3350 0.1 M MgCl2 2% (v/v) MPD

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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: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 50210 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.08 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.351 / Net I/σ(I): 5.11
Reflection shellResolution: 1.93→2.05 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 7962 / CC1/2: 0.551 / % 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: 1.93→16.48 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.05
RfactorNum. reflection% reflection
Rfree0.2163 2093 4.18 %
Rwork0.1795 --
obs0.181 50058 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→16.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 68 353 5238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.001
X-RAY DIFFRACTIONf_dihedral_angle_d17.56
X-RAY DIFFRACTIONf_chiral_restr0.051
X-RAY DIFFRACTIONf_plane_restr0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.32741350.27613101X-RAY DIFFRACTION97
1.97-2.020.3041380.27813161X-RAY DIFFRACTION100
2.02-2.080.30621380.25393154X-RAY DIFFRACTION100
2.08-2.140.3221390.24143164X-RAY DIFFRACTION100
2.14-2.210.24361380.22773157X-RAY DIFFRACTION100
2.21-2.290.24391390.20393179X-RAY DIFFRACTION99
2.29-2.380.25871380.20673162X-RAY DIFFRACTION99
2.38-2.480.26321380.18693174X-RAY DIFFRACTION100
2.48-2.620.21471400.17933209X-RAY DIFFRACTION100
2.62-2.780.22031370.16953175X-RAY DIFFRACTION100
2.78-2.990.19311410.16453231X-RAY DIFFRACTION100
2.99-3.290.21211400.15323216X-RAY DIFFRACTION100
3.29-3.760.16791420.13983246X-RAY DIFFRACTION100
3.76-4.720.14871410.13943228X-RAY DIFFRACTION99
4.72-16.480.17631490.15853408X-RAY DIFFRACTION100

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