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- PDB-8qwr: Crystal structure of CotB2 variant V80L -

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Basic information

Entry
Database: PDB / ID: 8qwr
TitleCrystal structure of CotB2 variant V80L
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 / Cyclooctat-9-en-7-ol synthase
Function and homology information
Biological speciesStreptomyces melanosporofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)74,2948
Polymers73,5692
Non-polymers7256
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-62 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.320, 100.570, 108.750
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: 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9K1X5
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 44.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 10 / Details: 0.1M CAPS pH 10.0, 19% PEG8000

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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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 72214 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 31.9 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.061 / Net I/σ(I): 22.9
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 11239 / CC1/2: 0.984 / Rrim(I) all: 0.521 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OMG

4omg


Resolution: 1.7→47.83 Å / SU ML: 0.1343 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 1986 2.76 %
Rwork0.1721 69928 -
obs0.1728 71914 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 46 334 4964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01045015
X-RAY DIFFRACTIONf_angle_d1.05386862
X-RAY DIFFRACTIONf_chiral_restr0.0614748
X-RAY DIFFRACTIONf_plane_restr0.0096892
X-RAY DIFFRACTIONf_dihedral_angle_d14.10641930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.24271490.21054911X-RAY DIFFRACTION99.06
1.74-1.790.28311310.20724931X-RAY DIFFRACTION99.12
1.79-1.840.24471350.19914915X-RAY DIFFRACTION99.41
1.84-1.90.22611430.19264927X-RAY DIFFRACTION99.45
1.9-1.970.19381430.18744949X-RAY DIFFRACTION99.49
1.97-2.050.25211370.18344952X-RAY DIFFRACTION99.32
2.05-2.140.1971390.17294945X-RAY DIFFRACTION99.67
2.14-2.250.19861440.16824981X-RAY DIFFRACTION99.71
2.25-2.40.21761440.17034976X-RAY DIFFRACTION99.61
2.4-2.580.16781390.1725016X-RAY DIFFRACTION99.81
2.58-2.840.18651440.17835024X-RAY DIFFRACTION99.88
2.84-3.250.20431480.18195039X-RAY DIFFRACTION99.75
3.25-4.10.19171420.15815096X-RAY DIFFRACTION99.85
4.1-47.830.17531480.16065266X-RAY DIFFRACTION98.9

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