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- PDB-2ju2: Minimized mean solution structure of the acyl carrier protein dom... -

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Basic information

Entry
Database: PDB / ID: 2ju2
TitleMinimized mean solution structure of the acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS)
ComponentsErythronolide synthase
KeywordsTRANSFERASE / carrier protein domain / modular polyketide synthase / alpha-helical bundle / Acyltransferase / Antibiotic biosynthesis / Multifunctional enzyme / NADP / Phosphopantetheine
Function / homology
Function and homology information


erythronolide synthase activity / 6-deoxyerythronolide-B synthase / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
CurL-like, PKS C-terminal / ACP-like / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase ...CurL-like, PKS C-terminal / ACP-like / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythronolide synthase EryA1
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsresidues 5-95 are identical to the DEBS residues 3318-3408 (EryA, EntrezProtein accession no. AAA26493)
Model type detailsminimized average
AuthorsAlekseyev, V.Y. / Liu, C.W. / Puglisi, J.D. / Khosla, C.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase.
Authors: Alekseyev, V.Y. / Liu, C.W. / Cane, D.E. / Puglisi, J.D. / Khosla, C.
History
DepositionAug 12, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythronolide synthase


Theoretical massNumber of molelcules
Total (without water)10,1611
Polymers10,1611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Erythronolide synthase / ORF 1 / 6-deoxyerythronolide B synthase I / DEBS 1


Mass: 10160.617 Da / Num. of mol.: 1 / Fragment: acyl carrier protein domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria)
Description: stop codon at the C-terminus, before the C-terminal His-tag present in the expression vector plasmid
Gene: eryA / Plasmid: pET28(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q03131, 6-deoxyerythronolide-B synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: residues 5-95 are identical to the DEBS residues 3318-3408 (EryA, EntrezProtein accession no. AAA26493)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C/15N NOESY
1313D (H)CCH-TOCSY
1413D HNHA
1512D 1H-15N HSQC
1613D HN(CA)CB
1713D C(CO)NH

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Sample preparation

DetailsContents: 0.8-1 mM [U-13C; U-15N] acyl carrier protein, 0.05 % sodium azide, 30 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMacyl carrier protein[U-13C; U-15N]1
0.05 %sodium azide1
30 mMsodium phosphate1
Sample conditionsIonic strength: 30 / pH: 5.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P. et al.structure solution
DYANA1.5Guntert, P. et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The standard simulated annealing protocol included as part of DYANA software was used to calculate a total of 50 structures, of which 30 structures with the lowest target function values ...Details: The standard simulated annealing protocol included as part of DYANA software was used to calculate a total of 50 structures, of which 30 structures with the lowest target function values were chosen for the solution structure ensemble. The helical regions of these 30 structures were superimposed and the mean structure was obtained using MOLMOL software, then subjected to the standard variable target function minimization implemented in DYANA. The resulting minimized mean structure is deposited here. The ensemble of 30 structures is deposited in the PDB entry 2ju1.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 1

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