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- PDB-8ysp: Crystal structure of a cyanobacteria type III polyketide synthase CylI -

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Basic information

Entry
Database: PDB / ID: 8ysp
TitleCrystal structure of a cyanobacteria type III polyketide synthase CylI
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
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 23, 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


Theoretical massNumber of molelcules
Total (without water)86,4552
Polymers86,4552
Non-polymers00
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-28 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.812, 110.274, 133.744
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M magnesium chloride

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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: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→22.06 Å / Num. obs: 49001 / % possible obs: 98.58 % / Redundancy: 4.7 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.997 / Net I/σ(I): 28.74
Reflection shellResolution: 2→2.071 Å / Mean I/σ(I) obs: 10.38 / Num. unique obs: 4853 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.06 Å / SU ML: 0.2773 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.5233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 2367 4.83 %
Rwork0.2254 46624 -
obs0.2276 48991 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 2→22.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5621 0 0 409 6030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00595726
X-RAY DIFFRACTIONf_angle_d0.87477781
X-RAY DIFFRACTIONf_chiral_restr0.051920
X-RAY DIFFRACTIONf_plane_restr0.008996
X-RAY DIFFRACTIONf_dihedral_angle_d5.3657776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.32581230.25932752X-RAY DIFFRACTION99.17
2.04-2.090.34591430.25142688X-RAY DIFFRACTION100
2.09-2.130.31611280.24182762X-RAY DIFFRACTION99.93
2.13-2.190.26251340.23752742X-RAY DIFFRACTION99.9
2.19-2.250.29921350.24342735X-RAY DIFFRACTION99.97
2.25-2.310.29611410.24552767X-RAY DIFFRACTION99.86
2.31-2.390.27051400.26092718X-RAY DIFFRACTION99.93
2.39-2.470.33941300.24592769X-RAY DIFFRACTION99.9
2.47-2.570.31351730.24022751X-RAY DIFFRACTION99.69
2.57-2.690.32391470.24522723X-RAY DIFFRACTION99.38
2.69-2.830.25881420.23512730X-RAY DIFFRACTION99.38
2.83-3.010.29471210.23142777X-RAY DIFFRACTION99.04
3.01-3.240.25451500.23192730X-RAY DIFFRACTION98.43
3.24-3.560.25021500.21252728X-RAY DIFFRACTION97.99
3.56-4.070.24321340.20572757X-RAY DIFFRACTION96.92
4.07-5.120.21041450.18552690X-RAY DIFFRACTION95.49
5.12-22.060.22711310.19452805X-RAY DIFFRACTION93.35

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