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- PDB-8yt0: Structure of CylI in complex with acyl-SNAC substrate -

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Basic information

Entry
Database: PDB / ID: 8yt0
TitleStructure of CylI in complex with acyl-SNAC substrate
ComponentsCylI
KeywordsTRANSFERASE / cyanobacteria / cylindrocyclophane / type III PKS
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid biosynthetic process / membrane
Similarity search - Function
FAE1/Type III polyketide synthase-like protein / FAE1/Type III polyketide synthase-like protein / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Biological speciesCylindrospermum licheniforme UTEX B 2014 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, H.Q. / Xiang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Key-Area Research and Development Program of Guangdong Province2020B0303070002 China
Shenzhen science and technology program20170330155106581 China
CitationJournal: Protein Sci. / Year: 2024
Title: Structural insights into type III polyketide synthase CylI from cylindrocyclophane biosynthesis.
Authors: Wang, H.Q. / Xiang, Z.
History
DepositionMar 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CylI
B: CylI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0704
Polymers86,4552
Non-polymers6162
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-28 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.829, 113.257, 134.255
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 CylI / Type III polyketide synthase


Mass: 43227.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cylindrospermum licheniforme UTEX B 2014 (bacteria)
Gene: cylI / Production host: Escherichia coli (E. coli) / References: UniProt: K7SIG4
#2: Chemical ChemComp-A1D7B / ~{S}-(2-acetamidoethyl) (6~{S})-6-chloranyldecanethioate


Mass: 307.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26ClNO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 27% PEG 4000, 0.09 M Tris-HCl, pH 8.0, 0.18 M magnesium chloride, 3% w/v 6-Aminohexanoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→22.34 Å / Num. obs: 59541 / % possible obs: 99.88 % / Redundancy: 9 % / Biso Wilson estimate: 13.38 Å2 / CC1/2: 0.999 / Net I/σ(I): 37.54
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 5871 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→22.34 Å / SU ML: 0.1753 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 2966 4.98 %
Rwork0.1759 56571 -
obs0.1775 59537 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5648 0 38 293 5979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755791
X-RAY DIFFRACTIONf_angle_d0.96997868
X-RAY DIFFRACTIONf_chiral_restr0.059928
X-RAY DIFFRACTIONf_plane_restr0.00811010
X-RAY DIFFRACTIONf_dihedral_angle_d5.8812797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.261370.20732679X-RAY DIFFRACTION99.93
1.93-1.960.24251240.18562648X-RAY DIFFRACTION100
1.96-20.24081430.17332628X-RAY DIFFRACTION100
2-2.040.22711490.17592682X-RAY DIFFRACTION100
2.04-2.080.20811340.17422640X-RAY DIFFRACTION100
2.08-2.130.22221530.17872682X-RAY DIFFRACTION100
2.13-2.170.23461290.17322641X-RAY DIFFRACTION99.96
2.17-2.230.24051290.17652707X-RAY DIFFRACTION100
2.23-2.290.20841490.18142632X-RAY DIFFRACTION100
2.29-2.360.22461340.18292673X-RAY DIFFRACTION100
2.36-2.430.24361520.18132685X-RAY DIFFRACTION100
2.43-2.520.22221410.17632658X-RAY DIFFRACTION100
2.52-2.620.19461380.18792690X-RAY DIFFRACTION100
2.62-2.740.2281510.19222679X-RAY DIFFRACTION100
2.74-2.880.20561460.19652700X-RAY DIFFRACTION100
2.88-3.060.21131250.19542717X-RAY DIFFRACTION100
3.06-3.30.18941470.18872692X-RAY DIFFRACTION99.96
3.3-3.630.20271390.16932729X-RAY DIFFRACTION99.97
3.63-4.150.18621480.15922744X-RAY DIFFRACTION100
4.15-5.220.16071400.14072770X-RAY DIFFRACTION99.86
5.22-22.340.17761580.17162895X-RAY DIFFRACTION99.67

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