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- PDB-8qws: Crystal structure of CotB2 variant V80L in complex with alendronate -

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Basic information

Entry
Database: PDB / ID: 8qws
TitleCrystal structure of CotB2 variant V80L in complex with alendronate
ComponentsCyclooctat-9-en-7-ol synthase
KeywordsLYASE / TERPENE SYNTHASE / CYCLOOCTATIN
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 / ACETATE ION / 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: 1.6 Å
AuthorsDimos, N. / Himpich, S. / Ringel, M. / Driller, R. / Major, D.T. / Brueck, T. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German-Israeli Foundation for Research and DevelopmentI-85-302.5-2019 Germany
CitationJournal: Chemcatchem / Year: 2024
Title: How Can the Diterpene Synthase CotB2V80L Alter the Product Profile?
Authors: Himpich, S. / Ringel, M. / Schwartz, R. / Dimos, N. / Driller, R. / Helmer, C.P.O. / Kumar Gupta, P. / Haack, M. / Thomas Major, D. / Bruck, T. / Loll, B.
History
DepositionOct 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)75,95634
Polymers73,5692
Non-polymers2,38732
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-106 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.173, 98.514, 107.417
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: 36784.551 Da / Num. of mol.: 2 / Mutation: V80L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria)
Gene: CotB2 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9K1X5

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Non-polymers , 8 types, 347 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 7 % PEG8000, 0.15 M Mgacetate, 10% ethylenglycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9766 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 86123 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 23.95 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.099 / Net I/σ(I): 16.5
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.54 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13768 / CC1/2: 0.99 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GGJ

6ggj


Resolution: 1.6→47.16 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2052 4287 5 %
Rwork0.1718 81508 -
obs0.1734 85795 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 148 315 5156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01165251
X-RAY DIFFRACTIONf_angle_d1.12657142
X-RAY DIFFRACTIONf_chiral_restr0.0607754
X-RAY DIFFRACTIONf_plane_restr0.0107927
X-RAY DIFFRACTIONf_dihedral_angle_d15.3282020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.3541400.35482664X-RAY DIFFRACTION98.52
1.62-1.640.35051410.3422688X-RAY DIFFRACTION99.61
1.64-1.660.36541400.32542659X-RAY DIFFRACTION99.4
1.66-1.680.3231410.31422690X-RAY DIFFRACTION99.37
1.68-1.70.30281420.30712708X-RAY DIFFRACTION99.23
1.7-1.720.30761380.2942639X-RAY DIFFRACTION99.5
1.72-1.750.31211440.27242725X-RAY DIFFRACTION99.41
1.75-1.770.31341400.26382651X-RAY DIFFRACTION99.32
1.77-1.80.29071420.2452697X-RAY DIFFRACTION99.02
1.8-1.830.2641420.21922675X-RAY DIFFRACTION99.3
1.83-1.860.26031390.21032701X-RAY DIFFRACTION99.4
1.86-1.90.25521410.20282691X-RAY DIFFRACTION99.68
1.9-1.930.22871430.19052705X-RAY DIFFRACTION99.62
1.93-1.970.19921400.17072695X-RAY DIFFRACTION99.23
1.97-2.020.21471410.16442667X-RAY DIFFRACTION99.57
2.02-2.060.21721430.15032730X-RAY DIFFRACTION99.52
2.06-2.110.18521410.15762700X-RAY DIFFRACTION99.44
2.11-2.170.20281420.15522693X-RAY DIFFRACTION99.3
2.17-2.240.20521430.15232710X-RAY DIFFRACTION99.69
2.24-2.310.19081420.14992694X-RAY DIFFRACTION99.61
2.31-2.390.18621450.1522738X-RAY DIFFRACTION99.65
2.39-2.490.18661430.15132711X-RAY DIFFRACTION99.76
2.49-2.60.19581440.15852746X-RAY DIFFRACTION99.9
2.6-2.740.19661450.1572739X-RAY DIFFRACTION99.9
2.74-2.910.21450.15162758X-RAY DIFFRACTION99.38
2.91-3.130.19871440.15632723X-RAY DIFFRACTION99.41
3.13-3.450.17881460.15662767X-RAY DIFFRACTION99.93
3.45-3.950.17851470.14222797X-RAY DIFFRACTION100
3.95-4.970.17651480.1422812X-RAY DIFFRACTION100
4.97-47.160.19751550.19662935X-RAY DIFFRACTION99.23

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