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- PDB-5yda: The crystal structure of the Acyl Transferase domain of SpnD -

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Basic information

Entry
Database: PDB / ID: 5yda
TitleThe crystal structure of the Acyl Transferase domain of SpnD
ComponentsPKS
KeywordsBIOSYNTHETIC PROTEIN / PKS / Acyl Transferase domain
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Thioesterase / Thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase ...Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Thioesterase / Thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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. / 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 / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces sp. CNQ431 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.353 Å
AuthorsLi, Y. / Qu, X.D. / Zhou, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin.
Authors: Li, Y. / Zhang, W. / Zhang, H. / Tian, W.Y. / Wu, L. / Wang, S.W. / Zheng, M.M. / Zhang, J.R. / Sun, C.H. / Deng, Z.X. / Sun, Y.H. / Qu, X.D. / Zhou, J.H.
History
DepositionSep 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PKS


Theoretical massNumber of molelcules
Total (without water)46,2481
Polymers46,2481
Non-polymers00
Water3,909217
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 area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.780, 109.780, 142.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

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Components

#1: Protein PKS


Mass: 46248.445 Da / Num. of mol.: 1 / Fragment: Acyl Transferase domain, UNP residues 457-861
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CNQ431 (bacteria) / Gene: spnD
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A0E3JLZ0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 4.42 Å3/Da / Density % sol: 72.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5M Lithium sulfate monohydrate, 0.1M Bis-Tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 36828 / % possible obs: 100 % / Redundancy: 25.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 49
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.692

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155phasing
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.10.1-2155refinement
RefinementResolution: 2.353→49.095 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.43
RfactorNum. reflection% reflection
Rfree0.2151 1811 4.92 %
Rwork0.1952 --
obs0.1962 36808 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.353→49.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 0 217 3270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083113
X-RAY DIFFRACTIONf_angle_d1.0594246
X-RAY DIFFRACTIONf_dihedral_angle_d19.8671883
X-RAY DIFFRACTIONf_chiral_restr0.058494
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3527-2.41630.26181450.2292612X-RAY DIFFRACTION100
2.4163-2.48740.22441270.22432658X-RAY DIFFRACTION100
2.4874-2.56770.28821570.21912648X-RAY DIFFRACTION100
2.5677-2.65950.26071420.2072625X-RAY DIFFRACTION100
2.6595-2.7660.26161370.21762667X-RAY DIFFRACTION100
2.766-2.89180.24861370.2142673X-RAY DIFFRACTION100
2.8918-3.04430.20891230.20462685X-RAY DIFFRACTION100
3.0443-3.2350.22011300.19822688X-RAY DIFFRACTION100
3.235-3.48470.22021190.19772683X-RAY DIFFRACTION100
3.4847-3.83530.20161360.18012721X-RAY DIFFRACTION100
3.8353-4.38990.18281350.16362721X-RAY DIFFRACTION100
4.3899-5.52960.18351510.17392739X-RAY DIFFRACTION100
5.5296-49.10580.20471720.20812877X-RAY DIFFRACTION99

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