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- PDB-9cbd: Pikromycin Thioesterase Domain -

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Basic information

Entry
Database: PDB / ID: 9cbd
TitlePikromycin Thioesterase Domain
ComponentsNarbonolide/10-deoxymethynolide synthase PikA4, module 6
KeywordsHYDROLASE / Polyketide synthase / PKS / Thioesterase / TE / Macrolactonization / Pikromycin
Function / homology
Function and homology information


10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / acyltransferase activity, transferring groups other than amino-acyl groups / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / : / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension ...Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / : / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / 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 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Narbonolide/10-deoxymethynolide synthase PikA4, module 6
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcCullough, T.M. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
CitationJournal: Acs Catalysis / Year: 2024
Title: Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation
Authors: McCullough, T.M. / Choudhary, V. / Akey, D.L. / Skiba, M.A. / Bernard, S.M. / Kittendorf, J.D. / Schmidt, J.J. / Sherman, D.H. / Smith, J.L.
History
DepositionJun 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Narbonolide/10-deoxymethynolide synthase PikA4, module 6
B: Narbonolide/10-deoxymethynolide synthase PikA4, module 6


Theoretical massNumber of molelcules
Total (without water)62,2822
Polymers62,2822
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-15 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.579, 105.932, 114.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Narbonolide/10-deoxymethynolide synthase PikA4, module 6 / Narbonolide/10-deoxymethynolide synthase PikAIV / Pikromycin polyketide synthase component PikAIV / ...Narbonolide/10-deoxymethynolide synthase PikAIV / Pikromycin polyketide synthase component PikAIV / Pikromycin PKS component PikAIV / Type I modular polyketide synthase PikAIV / PKS


Mass: 31140.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: pikAIV / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9ZGI2, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.2 M lithium chloride, 25% w/v PEG4000, 100 mM HEPES, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→48.04 Å / Num. obs: 48701 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 30777 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.038 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 2230 2.41 %
Rwork0.1975 --
obs0.1983 92404 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 0 305 4495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084300
X-RAY DIFFRACTIONf_angle_d0.8715860
X-RAY DIFFRACTIONf_dihedral_angle_d16.0882544
X-RAY DIFFRACTIONf_chiral_restr0.049628
X-RAY DIFFRACTIONf_plane_restr0.006794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04350.3161360.32115600X-RAY DIFFRACTION100
2.0435-2.0910.35431200.31315689X-RAY DIFFRACTION100
2.091-2.14330.34251410.30525581X-RAY DIFFRACTION100
2.1433-2.20130.27631440.29055677X-RAY DIFFRACTION100
2.2013-2.26610.331550.27195641X-RAY DIFFRACTION100
2.2661-2.33920.2671270.24535678X-RAY DIFFRACTION100
2.3392-2.42280.27581470.23875620X-RAY DIFFRACTION100
2.4228-2.51980.24911400.23585670X-RAY DIFFRACTION100
2.5198-2.63450.2511340.23035626X-RAY DIFFRACTION100
2.6345-2.77340.25781440.22355607X-RAY DIFFRACTION99
2.7734-2.94710.2771340.21655655X-RAY DIFFRACTION100
2.9471-3.17460.23581440.25630X-RAY DIFFRACTION100
3.1746-3.4940.25131500.19755627X-RAY DIFFRACTION100
3.494-3.99940.1881380.16655638X-RAY DIFFRACTION100
3.9994-5.03790.17611390.15265620X-RAY DIFFRACTION99
5.0379-48.0380.18671370.15825615X-RAY DIFFRACTION100

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