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- PDB-7ao1: Crystal structure of CotB2 variant W288F in complex with alendronate -

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Basic information

Entry
Database: PDB / ID: 7ao1
TitleCrystal structure of CotB2 variant W288F in complex with alendronate
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
4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / Cyclooctat-9-en-7-ol synthase
Similarity search - Component
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)74,52415
Polymers73,4632
Non-polymers1,06113
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-140 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.668, 57.096, 57.349
Angle α, β, γ (deg.)91.051, 116.314, 102.014
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 339 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl pH 8.5 20% (w/v) PEG4000 0.2 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: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 49054 / % possible obs: 88.9 % / Redundancy: 2.1 % / Biso Wilson estimate: 25.28 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7715 / CC1/2: 0.659 / Rrim(I) all: 0.746 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GGJ

6ggj


Resolution: 1.8→20.45 Å / SU ML: 0.2344 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.0155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 2097 4.28 %
Rwork0.1729 46923 -
obs0.1751 49020 89.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4878 0 60 326 5264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325256
X-RAY DIFFRACTIONf_angle_d1.24927160
X-RAY DIFFRACTIONf_chiral_restr0.0613766
X-RAY DIFFRACTIONf_plane_restr0.0079938
X-RAY DIFFRACTIONf_dihedral_angle_d21.07751953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.3311370.31113071X-RAY DIFFRACTION86.21
1.84-1.890.32141350.27213013X-RAY DIFFRACTION87.2
1.89-1.940.33471300.25412917X-RAY DIFFRACTION83.09
1.94-1.990.28271200.23852688X-RAY DIFFRACTION75.93
1.99-2.060.28731480.23383288X-RAY DIFFRACTION93.5
2.06-2.130.30431460.223282X-RAY DIFFRACTION94.18
2.13-2.220.27581490.19783325X-RAY DIFFRACTION94.53
2.22-2.320.27981460.19313275X-RAY DIFFRACTION94.11
2.32-2.440.26581470.17743304X-RAY DIFFRACTION93.42
2.44-2.590.23051460.17553258X-RAY DIFFRACTION92.58
2.59-2.790.20581450.17133230X-RAY DIFFRACTION92.36
2.79-3.070.21131400.16693153X-RAY DIFFRACTION90.29
3.07-3.520.22361340.16182975X-RAY DIFFRACTION84.71
3.52-4.420.17891340.1322998X-RAY DIFFRACTION85.11
4.42-20.450.16921400.13753146X-RAY DIFFRACTION89.81

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