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- PDB-7ao0: Crystal structure of CotB2 variant F107A in complex with alendronate -

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Basic information

Entry
Database: PDB / ID: 7ao0
TitleCrystal structure of CotB2 variant F107A 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: 1.93 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)74,56816
Polymers73,3892
Non-polymers1,18014
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-149 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.811, 98.050, 106.830
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

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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 / Mutation: F107A
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, 469 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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.: 455 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
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: 19.07 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.351 / Net I/σ(I): 5.11
Reflection shellResolution: 1.93→2.05 Å / Mean I/σ(I) obs: 1.08 / Num. unique obs: 7962 / CC1/2: 0.551 / Rrim(I) all: 1.804 / % possible all: 98.8

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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: 1.93→49.02 Å / SU ML: 0.2597 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2376 2096 4.18 %
Rwork0.1806 48032 -
obs0.1829 50128 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.3 Å2
Refinement stepCycle: LAST / Resolution: 1.93→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 68 455 5340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00885170
X-RAY DIFFRACTIONf_angle_d0.94327041
X-RAY DIFFRACTIONf_chiral_restr0.0516754
X-RAY DIFFRACTIONf_plane_restr0.0058911
X-RAY DIFFRACTIONf_dihedral_angle_d20.8071917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.30341350.26663104X-RAY DIFFRACTION97.12
1.97-2.020.31391390.26443164X-RAY DIFFRACTION99.88
2.02-2.080.31611380.23873163X-RAY DIFFRACTION99.64
2.08-2.140.31011380.22873163X-RAY DIFFRACTION99.73
2.14-2.210.26691390.21823171X-RAY DIFFRACTION99.61
2.21-2.290.25371390.19883173X-RAY DIFFRACTION99.19
2.29-2.380.2821380.20383175X-RAY DIFFRACTION99.04
2.38-2.490.32671390.18413172X-RAY DIFFRACTION99.73
2.49-2.620.231400.18433224X-RAY DIFFRACTION99.94
2.62-2.780.24541370.17493183X-RAY DIFFRACTION99.61
2.78-30.22461410.16763218X-RAY DIFFRACTION99.67
3-3.30.23361410.16213233X-RAY DIFFRACTION99.65
3.3-3.770.18221420.14813251X-RAY DIFFRACTION99.91
3.78-4.750.16771410.13363239X-RAY DIFFRACTION98.63
4.75-49.020.21921490.17623399X-RAY DIFFRACTION98.67

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