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- PDB-2mvu: Solution Structure of the 3,7-dioxo-octyl Actinorhodin Acyl Carri... -

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Basic information

Entry
Database: PDB / ID: 2mvu
TitleSolution Structure of the 3,7-dioxo-octyl Actinorhodin Acyl Carrier Protein from Streptomyces coelicolor
ComponentsActinorhodin polyketide synthase acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / Actinorhodin / ACP / biosynthetic intermediates / ligand recognition
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / antibiotic biosynthetic process / membrane / 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
Chem-SDO / Actinorhodin polyketide synthase acyl carrier protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDong, X. / Bailey, C. / Williams, C. / Crosby, J. / Simpson, T.J. / Willis, C.L. / Crump, M.P.
CitationJournal: To be Published
Title: ACP-ligand recognition: Selection of derivatized aromatic biosynthetic intermediates
Authors: Dong, X. / Bailey, C. / Williams, C. / Crosby, J. / Simpson, T.J. / Willis, C.L. / Crump, M.P.
History
DepositionOct 15, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _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)9,7222
Polymers9,2391
Non-polymers4831
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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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: ATCC BAA-471 / A3(2) / M145
Gene: Actinorhodin Acyl Carrier protein, SCBAC28G1.15, SCO5089
Plasmid: pET 11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02054
#2: Chemical ChemComp-SDO / N~3~-{(2S)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-{2-[(3,7-dioxooctyl)sulfanyl]ethyl}-beta-alaninamide


Mass: 482.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35N2O8PS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D H(CCO)NH

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Sample preparation

DetailsContents: 1-2 mM [U-98% 13C; U-98% 15N] protein, 20 mM potassium phosphate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-98% 13C; U-98% 15N]1-21
20 mMpotassium phosphate-21
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Unity / Manufacturer: Agilent / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJ4Variancollection
ARIALinge, O'Donoghue and Nilgesstructure solution
Analysis1.15CCPNchemical shift assignment
Analysis1.15CCPNdata analysis
Analysis1.15CCPNpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 20 LOWEST ENERGY STRUCTURES WERE FURTHER REFINED IN EXPLICIT WATER USING THE RECOORD PROTOCOL
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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