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- PDB-2k0x: The actinorhodin holo acyl carrier protein from S. coelicolor -

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Basic information

Entry
Database: PDB / ID: 2k0x
TitleThe actinorhodin holo acyl carrier protein from S. coelicolor
ComponentsActinorhodin polyketide synthase acyl carrier protein
KeywordsTRANSPORT PROTEIN / Acyl carrier protein / polyketide / holo / phosphopantetheine / Antibiotic biosynthesis
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / antibiotic biosynthetic process / 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
4'-PHOSPHOPANTETHEINE / Actinorhodin polyketide synthase acyl carrier protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsThis deposit is a set of twenty structures of the holo (phosphopantetheinylated) actinorhodin ...This deposit is a set of twenty structures of the holo (phosphopantetheinylated) actinorhodin polyketide acyl carrier protein (ACP). These datasets form a sister set to the recent apo- coordinates we deposited and can be used to directly compare the two forms.
AuthorsCrump, M.P. / Evans, S.E. / Williams, C.
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 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actinorhodin polyketide synthase acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5982
Polymers9,2391
Non-polymers3581
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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) / Strain: A3(2)
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. The protein was modified to the holo form using S. coelicolor ACPS and Enzyme CoA.
Gene: actI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q02054
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This deposit is a set of twenty structures of the holo (phosphopantetheinylated) actinorhodin polyketide acyl carrier protein (ACP). These datasets form a sister set to the recent apo- ...Details: This deposit is a set of twenty structures of the holo (phosphopantetheinylated) actinorhodin polyketide acyl carrier protein (ACP). These datasets form a sister set to the recent apo- coordinates we deposited and can be used to directly compare the two forms.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY
1313D 1H-15N NOESY
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D HNCO
181F1,F2 double filtered NOESY
191F1,F2 double filtered TOCSY
1101F2-filtered NOESY

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Sample preparation

DetailsContents: 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMact holo-acp[U-98% 13C; U-98% 15N]1
1 mMPhosphopantetheine side chain1
95 %H2O1
5 %D2O1
20 mMpotassium phosphate1
5 mMTCEP1
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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