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- PDB-7r0x: Structure of the branching thioesterase from oocydin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 7r0x
TitleStructure of the branching thioesterase from oocydin biosynthesis
ComponentsPolyketide synthase
KeywordsHYDROLASE / thioesterase / polyketide / acylation
Function / homology
Function and homology information


secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain ...Methyltransferase type 12 / Methyltransferase domain / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesSerratia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.83 Å
AuthorsFraley, A.E. / Piel, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)742739European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Structure of a Promiscuous Thioesterase Domain Responsible for Branching Acylation in Polyketide Biosynthesis.
Authors: Fraley, A.E. / Dieterich, C.L. / Mabesoone, M.F.J. / Minas, H.A. / Meoded, R.A. / Hemmerling, F. / Piel, J.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase


Theoretical massNumber of molelcules
Total (without water)41,1021
Polymers41,1021
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.818, 106.818, 78.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Polyketide synthase / OocS TEB / thioesterase


Mass: 41102.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: CT690_01900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A318P693
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.809M ammonium sulfate, 100mM HEPES pH 7.5, 4.14% PEG 8K (w/v), 3.95% PEG400 (v/v)

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.83→40.76 Å / Num. obs: 144817 / % possible obs: 99.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 64.4 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 12.3
Reflection shellResolution: 2.83→2.93 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.06 / Num. unique obs: 1055 / CC1/2: 0.597 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
XDSdata scaling
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.83→40.76 Å / SU ML: 0.4795 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 2041 9.91 %
Rwork0.2238 18552 -
obs0.2293 20593 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.38 Å2
Refinement stepCycle: LAST / Resolution: 2.83→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 0 39 2457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232480
X-RAY DIFFRACTIONf_angle_d0.51153359
X-RAY DIFFRACTIONf_chiral_restr0.036357
X-RAY DIFFRACTIONf_plane_restr0.0047435
X-RAY DIFFRACTIONf_dihedral_angle_d4.4097333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.890.37531380.40311231X-RAY DIFFRACTION98.92
2.9-2.970.38821320.32361230X-RAY DIFFRACTION99.71
2.97-3.050.39631440.31391239X-RAY DIFFRACTION100
3.05-3.140.3731360.29691242X-RAY DIFFRACTION100
3.14-3.240.27151360.29251234X-RAY DIFFRACTION100
3.24-3.350.35581290.30851227X-RAY DIFFRACTION99.71
3.35-3.490.38511340.25091245X-RAY DIFFRACTION99.86
3.49-3.640.2971380.22651203X-RAY DIFFRACTION99.93
3.65-3.840.24681360.2121258X-RAY DIFFRACTION99.86
3.84-4.080.22741440.18641229X-RAY DIFFRACTION99.85
4.08-4.390.2491290.17531249X-RAY DIFFRACTION99.71
4.39-4.840.20521300.18021245X-RAY DIFFRACTION100
4.84-5.530.25361360.20111222X-RAY DIFFRACTION100
5.53-6.970.28331500.23041257X-RAY DIFFRACTION100
6.97-40.760.26971290.18781241X-RAY DIFFRACTION99.93

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