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- PDB-5kbz: Structure of the PksA Product Template domain in complex with a p... -

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Basic information

Entry
Database: PDB / ID: 5kbz
TitleStructure of the PksA Product Template domain in complex with a phosphopantetheine mimetic
ComponentsNoranthrone synthase
KeywordsTRANSCRIPTION / Aflatoxin / Polyketide Synthase / Polyketide / Product Template / Dehydratase / Double Hot Dog Fold / Cyclase
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 / Polyketide synthase dehydratase / 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 ...Polyketide product template domain / Polyketide synthase dehydratase / 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 / Thiol Ester Dehydrase; Chain A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-3B2 / Norsolorinic acid synthase
Similarity search - Component
Biological speciesAspergillus parasiticus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsTsai, S.C. / Burkart, M.D. / Townsend, C.A. / Barajas, J.F. / Shakya, G. / Topper, C.L. / Moreno, G. / Jackson, D.R. / Rivera, H. / La Clair, J.J. / Vagstad, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 100738-02 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Polyketide mimetics yield structural and mechanistic insights into product template domain function in nonreducing polyketide synthases.
Authors: Barajas, J.F. / Shakya, G. / Moreno, G. / Rivera, H. / Jackson, D.R. / Topper, C.L. / Vagstad, A.L. / La Clair, J.J. / Townsend, C.A. / Burkart, M.D. / Tsai, S.C.
History
DepositionJun 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

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Assembly

Deposited unit
A: Noranthrone synthase
B: Noranthrone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3684
Polymers83,0922
Non-polymers1,2752
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-3 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.374, 90.530, 90.836
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 Noranthrone synthase / Aflatoxin biosynthesis polyketide synthase / PKS / Aflatoxin biosynthesis protein C / Polyketide synthase A


Mass: 41546.090 Da / Num. of mol.: 2 / Fragment: UNP residues 1305-1660
Source method: isolated from a genetically manipulated source
Details: Electron density for certain residues was not observed and therefore omitted from the model.
Source: (gene. exp.) Aspergillus parasiticus (mold) / Gene: pksL1, aflC, pksA / Plasmid: pET28b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q12053, noranthrone synthase
#2: Chemical ChemComp-3B2 / (14R)-14-hydroxy-15,15-dimethyl-1-[5-({[(5-methyl-1,2-oxazol-3-yl)methyl]sulfanyl}methyl)-1,2-oxazol-3-yl]-4,9,13-trioxo-2-thia-5,8,12-triazahexadecan-16-yl dihydrogen phosphate


Mass: 637.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H36N5O10PS2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.22M Ammonium Acetate, 22% PEG 3,350 pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 68415 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.2
Reflection shellResolution: 1.74→1.86 Å / Rmerge(I) obs: 0.451 / CC1/2: 0.902 / Rpim(I) all: 0.22

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HRR

3hrr


Resolution: 1.803→45.418 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 2018 2.95 %
Rwork0.1899 --
obs0.1908 68327 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.803→45.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 82 640 5645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075098
X-RAY DIFFRACTIONf_angle_d0.8856900
X-RAY DIFFRACTIONf_dihedral_angle_d16.0993056
X-RAY DIFFRACTIONf_chiral_restr0.053779
X-RAY DIFFRACTIONf_plane_restr0.005882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.803-1.84810.28641410.25054473X-RAY DIFFRACTION95
1.8481-1.8980.24291420.20954674X-RAY DIFFRACTION100
1.898-1.95390.20131420.20764684X-RAY DIFFRACTION100
1.9539-2.0170.25911450.19144719X-RAY DIFFRACTION100
2.017-2.0890.21791430.1984718X-RAY DIFFRACTION100
2.089-2.17270.25891440.19044703X-RAY DIFFRACTION100
2.1727-2.27160.24541450.19524719X-RAY DIFFRACTION100
2.2716-2.39130.21341450.1934712X-RAY DIFFRACTION100
2.3913-2.54110.21131410.19754734X-RAY DIFFRACTION100
2.5411-2.73730.23311420.19424752X-RAY DIFFRACTION100
2.7373-3.01270.2391360.20164771X-RAY DIFFRACTION100
3.0127-3.44850.22281500.19294800X-RAY DIFFRACTION100
3.4485-4.34430.18731440.16774833X-RAY DIFFRACTION100
4.3443-45.43240.19731580.17975017X-RAY DIFFRACTION100

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