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- PDB-9rp1: Ensemble refined structure of CotB2 in complex with alendronate -

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Basic information

Entry
Database: PDB / ID: 9rp1
TitleEnsemble refined structure of CotB2 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: 2.1 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 in complex with alendronate
Authors: Helmer, C.P.O. / Loll, B.
#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

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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)74,17710
Polymers73,5412
Non-polymers6368
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.380, 56.460, 56.930
Angle α, β, γ (deg.)91.82, 101.66, 115.93
Int Tables number1
Space group name H-MP1
Number of models23

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Components

#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 DH5[alpha] (bacteria) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase
#2: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 26% (v/v) polyethylene glycol 4000, 100 mM Tris at pH 8.5, 150 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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 33594 / % possible obs: 99.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 28.06 Å2 / Rrim(I) all: 0.14 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2805 / Rrim(I) all: 0.922 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.83 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.86
RfactorNum. reflection% reflection
Rfree0.2124 1680 5 %
Rwork0.1731 --
obs0.1751 33590 99.31 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4734 0 34 211 4979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.939
X-RAY DIFFRACTIONf_dihedral_angle_d17.22
X-RAY DIFFRACTIONf_chiral_restr0.05
X-RAY DIFFRACTIONf_plane_restr0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.3041400.2662665X-RAY DIFFRACTION99
2.16-2.230.29511390.24042647X-RAY DIFFRACTION99
2.23-2.310.28451410.22282660X-RAY DIFFRACTION99
2.31-2.40.25171400.20032660X-RAY DIFFRACTION99
2.4-2.510.31471400.19362660X-RAY DIFFRACTION100
2.51-2.640.20471390.1942654X-RAY DIFFRACTION100
2.64-2.810.25351420.18742684X-RAY DIFFRACTION99
2.81-3.030.23351380.17842638X-RAY DIFFRACTION99
3.03-3.330.211420.17122688X-RAY DIFFRACTION100
3.33-3.810.20071390.15132640X-RAY DIFFRACTION99
3.81-4.790.15521400.13972669X-RAY DIFFRACTION100
4.79-19.830.16931400.14942645X-RAY DIFFRACTION99

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