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- PDB-9lsd: Crystal structure of a polyketide cyclase FasU from Streptomyces ... -

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Basic information

Entry
Database: PDB / ID: 9lsd
TitleCrystal structure of a polyketide cyclase FasU from Streptomyces kanamyceticus
ComponentsAntibiotic biosynthesis monooxygenase
KeywordsBIOSYNTHETIC PROTEIN / polyketide / cyclase
Function / homologyABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel / monooxygenase activity / 2-(2-ETHOXYETHOXY)ETHANOL / Antibiotic biosynthesis monooxygenase
Function and homology information
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLuo, S. / Zhu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: A Stereoselective Decarboxylative Aromatase/Cyclase Directs the Biosynthesis of an Axially Chiral Biphenyl Framework in Fasamycin.
Authors: Jiang, K. / Zhu, C. / Yan, X. / Li, G. / Lin, Z. / Deng, Z. / Luo, S. / Qu, X.
History
DepositionFeb 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibiotic biosynthesis monooxygenase
B: Antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9395
Polymers27,6472
Non-polymers2933
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-25 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.669, 85.669, 63.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Antibiotic biosynthesis monooxygenase


Mass: 13823.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kanamyceticus (bacteria) / Gene: CP970_07265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5J6G7S2
#2: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 200 mM Magnesium chloride, 100 mM Tris base/ Hydrochloric acid, 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.01→32.16 Å / Num. obs: 17734 / % possible obs: 99.5 % / Redundancy: 5.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.128 / Net I/σ(I): 8.25
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.01-2.130.48928570.8960.5441
2.13-2.270.33526580.930.3751
2.27-2.460.25925050.9530.2871
2.46-2.690.19923220.9720.2221
2.69-3.010.14220800.9790.161
3.01-3.470.1118360.9820.1231
3.47-4.240.09315770.9780.1051
4.24-5.980.0912110.9840.1011
5.98-32.160.0766880.9930.0851

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→32.01 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 897 5.08 %
Rwork0.1857 --
obs0.1879 17648 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 19 151 1905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071815
X-RAY DIFFRACTIONf_angle_d0.7992457
X-RAY DIFFRACTIONf_dihedral_angle_d32.965250
X-RAY DIFFRACTIONf_chiral_restr0.053257
X-RAY DIFFRACTIONf_plane_restr0.005327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.140.33081400.22412777X-RAY DIFFRACTION100
2.14-2.30.29331320.21572798X-RAY DIFFRACTION100
2.3-2.530.27711400.21482807X-RAY DIFFRACTION100
2.53-2.90.26461670.21432757X-RAY DIFFRACTION100
2.9-3.650.20921530.1782794X-RAY DIFFRACTION99
3.65-32.010.1941650.16092818X-RAY DIFFRACTION99

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