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- PDB-8yw7: Structure of CylI in complex with resorcinol product -

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Basic information

Entry
Database: PDB / ID: 8yw7
TitleStructure of CylI in complex with resorcinol product
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: 2 Å
AuthorsWang, H.Q. / Xiang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Shenzhen science and technology program20170330155106581 China
Key-Area Research and Development Program of Guangdong Province2020B0303070002 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 30, 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)86,7253
Polymers86,4552
Non-polymers2711
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-27 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.788, 112.822, 134.128
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-A1D7F / 5-[(2~{S},7~{R})-7-chloranyl-2-methyl-octyl]benzene-1,3-diol


Mass: 270.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23ClO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 27% PEG 4000, 0.09 M Tris-HCl, pH 8.5, 0.18 M magnesium chloride, 3% w/v D-Sorbitol

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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: May 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→22.39 Å / Num. obs: 50885 / % possible obs: 99.85 % / Redundancy: 9.9 % / Biso Wilson estimate: 15.34 Å2 / CC1/2: 0.998 / Net I/σ(I): 19.49
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 5003 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.39 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 2486 4.89 %
Rwork0.176 48395 -
obs0.1779 50881 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.58 Å2
Refinement stepCycle: LAST / Resolution: 2→22.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5671 0 18 550 6239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675797
X-RAY DIFFRACTIONf_angle_d0.8587886
X-RAY DIFFRACTIONf_chiral_restr0.0531932
X-RAY DIFFRACTIONf_plane_restr0.0071013
X-RAY DIFFRACTIONf_dihedral_angle_d5.2695790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.24131460.18682650X-RAY DIFFRACTION99.79
2.04-2.080.25171300.18362617X-RAY DIFFRACTION100
2.08-2.130.22041220.18212690X-RAY DIFFRACTION100
2.13-2.170.22541210.17822645X-RAY DIFFRACTION99.96
2.17-2.230.22371410.18582679X-RAY DIFFRACTION100
2.23-2.290.22721190.18522634X-RAY DIFFRACTION100
2.29-2.360.22721490.18962662X-RAY DIFFRACTION100
2.36-2.430.25281490.18472670X-RAY DIFFRACTION100
2.43-2.520.22831340.17922651X-RAY DIFFRACTION100
2.52-2.620.21311290.1852691X-RAY DIFFRACTION100
2.62-2.740.23661480.18252663X-RAY DIFFRACTION100
2.74-2.880.21291510.17972683X-RAY DIFFRACTION100
2.88-3.060.20781310.1842693X-RAY DIFFRACTION100
3.06-3.30.21541320.17692698X-RAY DIFFRACTION99.96
3.3-3.630.2231470.16632703X-RAY DIFFRACTION100
3.63-4.150.1851350.16052726X-RAY DIFFRACTION99.93
4.15-5.220.17861360.15242762X-RAY DIFFRACTION99.79
5.22-22.390.20831660.18472878X-RAY DIFFRACTION99.71

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