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- PDB-6obt: Structural insights into dehydratase substrate selection for the ... -

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Entry
Database: PDB / ID: 6obt
TitleStructural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
ComponentsBorrelidin polyketide synthase, type I
KeywordsLYASE / Polyketide / Dehydratase / Borrelidin / Fluvirucin
Function / homology
Function and homology information


transaminase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dehydratase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension ...Polyketide synthase dehydratase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / 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 / 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 / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Borrelidin polyketide synthase, type I
Similarity search - Component
Biological speciesStreptomyces parvulus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMcAndrew, R.P. / Barajas, J.F. / Pereira, J.H. / Keasling, J.D. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: J Ind Microbiol Biotechnol. / Year: 2019
Title: Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases.
Authors: Barajas, J.F. / McAndrew, R.P. / Thompson, M.G. / Backman, T.W.H. / Pang, B. / de Rond, T. / Pereira, J.H. / Benites, V.T. / Martin, H.G. / Baidoo, E.E.K. / Hillson, N.J. / Adams, P.D. / Keasling, J.D.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Borrelidin polyketide synthase, type I


Theoretical massNumber of molelcules
Total (without water)33,7581
Polymers33,7581
Non-polymers00
Water86548
1
A: Borrelidin polyketide synthase, type I

A: Borrelidin polyketide synthase, type I


Theoretical massNumber of molelcules
Total (without water)67,5152
Polymers67,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1990 Å2
ΔGint-6 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.210, 63.350, 40.670
Angle α, β, γ (deg.)90.00, 100.44, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Borrelidin polyketide synthase, type I


Mass: 33757.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces parvulus (bacteria) / Gene: borA3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70I00
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.20 M MgCl2, 0.10 M Tris pH 8.5, and 29% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30.9 Å / Num. obs: 24737 / % possible obs: 96.2 % / Biso Wilson estimate: 33.27 Å2
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
PHENIX1.15rc3_3435refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LN9

4ln9


Resolution: 1.8→30.89 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.232 1245 5.04 %
Rwork0.203 --
obs-24725 98.3 %
Displacement parametersBiso mean: 56.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 463 48 2080
LS refinement shellResolution: 1.8→1.87 Å
RfactorNum. reflection% reflection
Rfree0.3775 130 -
Rwork0.3636 2595 -
obs--97.88 %

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