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- PDB-3ils: The Thioesterase Domain from PksA -

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Basic information

Entry
Database: PDB / ID: 3ils
TitleThe Thioesterase Domain from PksA
ComponentsAflatoxin biosynthesis polyketide synthase
KeywordsHYDROLASE / a/b hydrolase / thioesterase / norsolorinic acid / aflatoxin / PksA / polyketide / Acyltransferase / Multifunctional enzyme / Phosphopantetheine
Function / homology
Function and homology information


noranthrone synthase / aflatoxin biosynthetic process / norsolorinate anthrone synthase activity / phosphopantetheine binding / identical protein binding
Similarity search - Function
Polyketide product template domain / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide product template domain / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain superfamily / 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 / 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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Norsolorinic acid synthase
Similarity search - Component
Biological speciesAspergillus parasiticus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKorman, T.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and function of an iterative polyketide synthase thioesterase domain catalyzing Claisen cyclization in aflatoxin biosynthesis.
Authors: Korman, T.P. / Crawford, J.M. / Labonte, J.W. / Newman, A.G. / Wong, J. / Townsend, C.A. / Tsai, S.C.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: Aflatoxin biosynthesis polyketide synthase


Theoretical massNumber of molelcules
Total (without water)29,1681
Polymers29,1681
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.934, 66.941, 67.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aflatoxin biosynthesis polyketide synthase / PKS


Mass: 29167.549 Da / Num. of mol.: 1 / Fragment: PksA Thioesterase Domain residues 1845-2109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus parasiticus (mold) / Gene: PksA, pksL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12053
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate, 30% PEG 4K, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9648, 0.98, 0.9802
SYNCHROTRONALS 5.0.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 27, 2007
MARMOSAIC 325 mm CCD2CCDFeb 23, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)MADMx-ray1
2Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96481
20.981
30.98021
411
Reflection twinOperator: k,h,-l / Fraction: 0.42
ReflectionResolution: 1.68→50 Å / Num. obs: 35395 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Χ2: 1.213 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.68-1.745.30.3332471.04192.5
1.74-1.816.20.26935211.701100
1.81-1.897.10.20334961.03100
1.89-1.997.30.14735181.21100
1.99-2.127.30.10935371.421100
2.12-2.287.30.08235441.217100
2.28-2.517.30.06635441.374100
2.51-2.877.20.05235751.014100
2.87-3.627.20.03936171.063100
3.62-506.80.03737961.07399.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 305
RfactorNum. reflection% reflection
Rfree0.208 1662 4.9 %
Rwork0.178 --
obs-33560 98 %
Solvent computationBsol: 39.882 Å2
Displacement parametersBiso max: 199.99 Å2 / Biso mean: 18.404 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å20 Å2
2--0.732 Å20 Å2
3----5.172 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 0 171 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0051.5
X-RAY DIFFRACTIONc_scbond_it1.5522
X-RAY DIFFRACTIONc_mcangle_it1.4452
X-RAY DIFFRACTIONc_scangle_it2.1332.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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