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- PDB-2k0y: The actinorhodin apo acyl carrier protein from S. coelicolor -

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Basic information

Entry
Database: PDB / ID: 2k0y
TitleThe actinorhodin apo acyl carrier protein from S. coelicolor
ComponentsActinorhodin polyketide synthase acyl carrier protein
KeywordsTRANSPORT PROTEIN / Acyl carrier Protein / Actinorhodin / Polyketide / Antibiotic / Antibiotic biosynthesis / Phosphopantetheine
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / antibiotic biosynthetic process / acyl carrier activity / cytosol
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Actinorhodin polyketide synthase acyl carrier protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsThis is an ensemble of 20 NMR structures, ARIA 1.2 restraint files (ambiguous and non-ambiguous ...This is an ensemble of 20 NMR structures, ARIA 1.2 restraint files (ambiguous and non-ambiguous NOEs, TALOS restraints and J-coupling restraints. Chemical shift data has also been deposited for 1H, 15N and 13C.
AuthorsCrump, M.P. / Evans, S.E. / Christopher, W.
CitationJournal: Chembiochem / Year: 2008
Title: An ACP Structural Switch: Conformational Differences between the Apo and Holo Forms of the Actinorhodin Polyketide Synthase Acyl Carrier Protein.
Authors: Evans, S.E. / Williams, C. / Arthur, C.J. / Burston, S.G. / Simpson, T.J. / Crosby, J. / Crump, M.P.
History
DepositionFeb 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actinorhodin polyketide synthase acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)9,2391
Polymers9,2391
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Actinorhodin polyketide synthase acyl carrier protein / ACP / actI ORF3


Mass: 9239.177 Da / Num. of mol.: 1 / Mutation: C17S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria)
Description: Actinorhodin acyl carrier protein (act ACP) from S. coelicolor was heterologously overexpressed in its apo form in E. coli BL21 (DE3) cells. These cells contained the plasmid pET11c C17S ...Description: Actinorhodin acyl carrier protein (act ACP) from S. coelicolor was heterologously overexpressed in its apo form in E. coli BL21 (DE3) cells. These cells contained the plasmid pET11c C17S act ACP (courtesy of Dr. Tom Nicholson). This IPTG inducible vector is both easier to use and more reliable than the heat inducible pT7-7 version originally constructed.
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q02054

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This is an ensemble of 20 NMR structures, ARIA 1.2 restraint files (ambiguous and non-ambiguous NOEs, TALOS restraints and J-coupling restraints. Chemical shift data has also been deposited for 1H, 15N and 13C.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D HNHA
1713D 1H-15N NOESY
1813D 1H-13C NOESY
NMR detailsText: The structure was determined using a combination of NOE data (ambiguous and unambiguous as determined by ARIA) combined with J-coupling and TALOS dihedral restraints

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Sample preparation

DetailsContents: 1-2 mM [U-98% 13C; U-98% 15N] act ACP, 5% D2O, 95% H2O, 20 mM potassium phosphate, 1 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMact ACP[U-98% 13C; U-98% 15N]1
5 %D2O1
95 %H2O1
20 mMpotassium phosphate1
1 mMsodium azide1
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesprocessing
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: All structure calculations were carried out using the Ambiguous Restraints for Iterative Assignment of NOEs (ARIA) protocol Version 1.2, which includes an algorithm that attempts to correct ...Details: All structure calculations were carried out using the Ambiguous Restraints for Iterative Assignment of NOEs (ARIA) protocol Version 1.2, which includes an algorithm that attempts to correct for the effects of spin diffusion, was use. Torsion Angle Likelihood Obtained from Shift and sequence similarity (TALOS) and was used to predict φ and ψ dihedral angle restraints. Initially, structure calculation runs contained 8 iterations of 20 structures each, with the best 7 structures in each iteration (sorted according to total energy) being used for analysis and assignment. The number of dynamics steps was increased over default values to 20000 and 16000 for the first and second cooling stages respectively. After each run, violated restraints were checked, and those arising from noise peaks or incorrect assignments were removed/reassigned. Final ensembles of 100 structures were calculated from calibrated restraint tables. The 20 best structures (sorted according to total energy) were selected for water refinement. Water refined structures were calculated using the slightly modified refinement script applied to the RECOORD database. PROCHECK and WHATCHECK and quality indicators were compared to the average values for the RECOORD database of protein NMR structures.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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