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- PDB-7ao3: Crystal structure of CotB2 variant F149L in complex with alendronate -

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Basic information

Entry
Database: PDB / ID: 7ao3
TitleCrystal structure of CotB2 variant F149L 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: 1.45 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)74,65316
Polymers73,4732
Non-polymers1,18014
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-150 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.580, 57.210, 57.630
Angle α, β, γ (deg.)90.797, 116.111, 102.208
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: 36736.508 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 BL21 (bacteria) / References: UniProt: C9K1X5, cyclooctat-9-en-7-ol synthase

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Non-polymers , 5 types, 482 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 / Comment: medication*YM
#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.: 468 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl pH 8.5 28% (w/v) PEG4000 0.15 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 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 104729 / % possible obs: 98.8 % / Redundancy: 5 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.059 / Net I/σ(I): 15.8
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7681 / CC1/2: 0.6 / Rrim(I) all: 1.178 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GGJ

6ggj


Resolution: 1.45→38.27 Å / SU ML: 0.1553 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.2877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1776 5236 5 %
Rwork0.1378 99484 -
obs0.1397 104720 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.07 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4865 0 68 468 5401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01235276
X-RAY DIFFRACTIONf_angle_d1.2217199
X-RAY DIFFRACTIONf_chiral_restr0.095773
X-RAY DIFFRACTIONf_plane_restr0.0079935
X-RAY DIFFRACTIONf_dihedral_angle_d19.74391961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.30081740.26783295X-RAY DIFFRACTION97.53
1.47-1.480.27681700.24013244X-RAY DIFFRACTION97.99
1.48-1.50.2611730.223285X-RAY DIFFRACTION98.38
1.5-1.520.26951740.21053300X-RAY DIFFRACTION98.41
1.52-1.540.2781750.20423323X-RAY DIFFRACTION98.42
1.54-1.560.24791710.2053262X-RAY DIFFRACTION98.51
1.56-1.580.24471750.17383321X-RAY DIFFRACTION98.67
1.58-1.610.22731740.16443295X-RAY DIFFRACTION98.8
1.61-1.630.22421750.15153341X-RAY DIFFRACTION98.65
1.63-1.660.19011720.14073258X-RAY DIFFRACTION98.71
1.66-1.690.18461760.13273338X-RAY DIFFRACTION98.9
1.69-1.720.20121740.13563309X-RAY DIFFRACTION99.12
1.72-1.750.19981750.13433337X-RAY DIFFRACTION98.87
1.75-1.790.21191760.13483328X-RAY DIFFRACTION99.18
1.79-1.830.21371710.14413262X-RAY DIFFRACTION99.13
1.83-1.870.21591760.14433330X-RAY DIFFRACTION99.07
1.87-1.920.18921760.1313362X-RAY DIFFRACTION99.35
1.92-1.970.18961760.13123325X-RAY DIFFRACTION99.43
1.97-2.030.19171730.13273295X-RAY DIFFRACTION99.26
2.03-2.090.18581750.13213321X-RAY DIFFRACTION99.46
2.09-2.170.17111750.12533333X-RAY DIFFRACTION99.55
2.17-2.250.16371760.12153349X-RAY DIFFRACTION99.55
2.25-2.360.17011760.12053339X-RAY DIFFRACTION99.52
2.36-2.480.17071750.12583322X-RAY DIFFRACTION99.66
2.48-2.630.16741760.12943342X-RAY DIFFRACTION99.74
2.63-2.840.18821760.1373348X-RAY DIFFRACTION99.86
2.84-3.120.18741760.14263334X-RAY DIFFRACTION99.63
3.12-3.570.16321750.13913340X-RAY DIFFRACTION99.38
3.58-4.50.13351760.11723329X-RAY DIFFRACTION99.69
4.5-38.270.14771740.13733317X-RAY DIFFRACTION99.12

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