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- PDB-7ao5: Crystal structure of CotB2 variant W288F -

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Basic information

Entry
Database: PDB / ID: 7ao5
TitleCrystal structure of CotB2 variant W288F
ComponentsCyclooctat-9-en-7-ol synthase
KeywordsLYASE / TERPENE SYNTHASE / CYCLOOCTATIN
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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsDimos, N. / Driller, R. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German-Israeli Foundation for Research and DevelopmentI-85-302.5-2019 Germany
CitationJournal: 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. / Bruck, T. / Loll, B. / Major, D.T.
History
DepositionOct 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)73,9159
Polymers73,4632
Non-polymers4527
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-84 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.117, 107.575, 61.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 36731.484 Da / Num. of mol.: 2 / Mutation: W288F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria)
Gene: CotB2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl pH 8.5 13.5% (w/v) PEG3350 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 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: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 42357 / % possible obs: 99.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.252 / Net I/σ(I): 6
Reflection shellResolution: 2.06→2.18 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6752 / CC1/2: 0.5 / Rrim(I) all: 1.663 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OMG

4omg


Resolution: 2.06→47.49 Å / SU ML: 0.2742 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 2098 4.96 %
Rwork0.1834 40188 -
obs0.1862 42286 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.08 Å2
Refinement stepCycle: LAST / Resolution: 2.06→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 28 343 4915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014855
X-RAY DIFFRACTIONf_angle_d0.98696602
X-RAY DIFFRACTIONf_chiral_restr0.0501711
X-RAY DIFFRACTIONf_plane_restr0.0069863
X-RAY DIFFRACTIONf_dihedral_angle_d15.7711669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.36791380.30962629X-RAY DIFFRACTION98.82
2.11-2.160.31691380.28832649X-RAY DIFFRACTION99.82
2.16-2.220.35181380.2572648X-RAY DIFFRACTION99.79
2.22-2.280.29491380.24582664X-RAY DIFFRACTION99.72
2.28-2.360.31941380.22462632X-RAY DIFFRACTION99.93
2.36-2.440.29971380.21122643X-RAY DIFFRACTION99.78
2.44-2.540.31391400.20542674X-RAY DIFFRACTION99.89
2.54-2.660.2621380.19512661X-RAY DIFFRACTION99.86
2.66-2.80.23681410.18482689X-RAY DIFFRACTION99.89
2.8-2.970.2171400.17542691X-RAY DIFFRACTION99.72
2.97-3.20.22641400.17272674X-RAY DIFFRACTION99.36
3.2-3.520.1991400.17022681X-RAY DIFFRACTION99.54
3.52-4.030.20691410.14632710X-RAY DIFFRACTION99.65
4.03-5.080.20591440.14022743X-RAY DIFFRACTION99.38
5.08-47.490.19841460.16862800X-RAY DIFFRACTION96.97

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