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- PDB-6kog: Ketosynthase domain in tenuazonic acid synthetase 1 (TAS1). -

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Basic information

Entry
Database: PDB / ID: 6kog
TitleKetosynthase domain in tenuazonic acid synthetase 1 (TAS1).
ComponentsHybrid PKS-NRPS synthetase TAS1
KeywordsBIOSYNTHETIC PROTEIN / Ketosynthase domain / cyclization / tetramic acid ring formation / NRPS-PKS hybrid enzyme / TOXIN
Function / homology
Function and homology information


tenuazonic acid synthetase / ligase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Beta-ketoacyl synthase ...Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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
Similarity search - Domain/homology
Hybrid PKS-NRPS synthetase TAS1
Similarity search - Component
Biological speciesPyricularia oryzae 70-15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsYun, C.S. / Nishimoto, K. / Motoyama, T. / Hino, T. / Nagano, S. / Osada, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
Japan Society for the Promotion of Science (JSPS)17H05444 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Unique features of the ketosynthase domain in a nonribosomal peptide synthetase-polyketide synthase hybrid enzyme, tenuazonic acid synthetase 1.
Authors: Yun, C.S. / Nishimoto, K. / Motoyama, T. / Shimizu, T. / Hino, T. / Dohmae, N. / Nagano, S. / Osada, H.
History
DepositionAug 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Hybrid PKS-NRPS synthetase TAS1
B: Hybrid PKS-NRPS synthetase TAS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2234
Polymers96,0352
Non-polymers1882
Water12,484693
1
A: Hybrid PKS-NRPS synthetase TAS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1102
Polymers48,0181
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-1 kcal/mol
Surface area17130 Å2
MethodPISA
2
B: Hybrid PKS-NRPS synthetase TAS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1142
Polymers48,0181
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.633, 99.136, 127.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Hybrid PKS-NRPS synthetase TAS1 / Tenuazonic acid synthase 1


Mass: 48017.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae 70-15 (fungus) / Strain: 70-15 / Gene: TAS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS
References: UniProt: G4N137, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsSince the amino acid sequence of the crystalized TAS KS was deduced from cDNA, the sample sequence ...Since the amino acid sequence of the crystalized TAS KS was deduced from cDNA, the sample sequence should be correct for G4N137. Therefore, the authors state that the conflicts are due to the error in database,

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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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 120 mM NaCl, 1.65 M Ammonium sulfate, 0.1 M MES-NaOH pH 6.5, 5% Methanol

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.575→49.568 Å / Num. obs: 129538 / % possible obs: 80.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.63 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.61
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 87079 / CC1/2: 0.663 / % possible all: 35

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless1.11.4data scaling
pointless1.11.4data scaling
PHASER2.7.17phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZ0

4mz0


Resolution: 1.68→49.568 Å / SU ML: 0.1622 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2594
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1924 5763 5.07 %
Rwork0.1646 107839 -
obs0.166 113602 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.63 Å2
Refinement stepCycle: LAST / Resolution: 1.68→49.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 11 693 6941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01536420
X-RAY DIFFRACTIONf_angle_d1.32268754
X-RAY DIFFRACTIONf_chiral_restr0.09071002
X-RAY DIFFRACTIONf_plane_restr0.0091170
X-RAY DIFFRACTIONf_dihedral_angle_d22.0025940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.28811600.2653063X-RAY DIFFRACTION84.99
1.7-1.720.30311880.24253220X-RAY DIFFRACTION89.73
1.72-1.740.25411810.23973338X-RAY DIFFRACTION93.17
1.74-1.760.24921920.22653459X-RAY DIFFRACTION96.79
1.76-1.790.21731580.21943595X-RAY DIFFRACTION98.04
1.79-1.810.25151850.20923572X-RAY DIFFRACTION98.89
1.81-1.840.24472040.20333582X-RAY DIFFRACTION99.5
1.84-1.860.20071760.19363572X-RAY DIFFRACTION99.92
1.86-1.890.22811840.17823652X-RAY DIFFRACTION99.97
1.89-1.920.19861900.17313611X-RAY DIFFRACTION99.97
1.92-1.960.20771780.16243630X-RAY DIFFRACTION100
1.96-1.990.19482020.16083630X-RAY DIFFRACTION100
1.99-2.030.17782020.1583580X-RAY DIFFRACTION100
2.03-2.070.20732070.15523605X-RAY DIFFRACTION99.97
2.07-2.120.17881970.15283626X-RAY DIFFRACTION100
2.12-2.170.20882030.15323613X-RAY DIFFRACTION100
2.17-2.220.1912010.15073624X-RAY DIFFRACTION99.95
2.22-2.280.18921850.15753637X-RAY DIFFRACTION100
2.28-2.350.19112050.15763624X-RAY DIFFRACTION99.97
2.35-2.420.1971990.16173611X-RAY DIFFRACTION99.95
2.42-2.510.20071940.16213629X-RAY DIFFRACTION100
2.51-2.610.19591950.16763669X-RAY DIFFRACTION99.87
2.61-2.730.18572090.16633631X-RAY DIFFRACTION99.97
2.73-2.870.1872080.16353640X-RAY DIFFRACTION99.97
2.87-3.050.21491820.16553674X-RAY DIFFRACTION100
3.05-3.290.19071940.15333674X-RAY DIFFRACTION99.92
3.29-3.620.15871900.1463704X-RAY DIFFRACTION99.97
3.62-4.140.16821780.14443731X-RAY DIFFRACTION99.97
4.14-5.220.16021950.14683752X-RAY DIFFRACTION99.92
5.22-49.570.20342210.19383891X-RAY DIFFRACTION99.71

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