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- PDB-2fvf: Structure of 10:0-ACP (protein with docked fatty acid) -

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Basic information

Entry
Database: PDB / ID: 2fvf
TitleStructure of 10:0-ACP (protein with docked fatty acid)
ComponentsAcyl Carrier Protein
KeywordsBIOSYNTHETIC PROTEIN / 4-helix bundle
Function / homology
Function and homology information


phosphopantetheine binding / acyl carrier activity / chloroplast
Similarity search - Function
Acyl carrier protein, chloroplastic / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily ...Acyl carrier protein, chloroplastic / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / 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
DECANOIC ACID / 4'-PHOSPHOPANTETHEINE / Acyl carrier protein 1, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodSOLUTION NMR / Initial structure from torsion angle dynamics (in CYANA). Fatty acid, phosphopantetheine were added, docked using ambiguous distance restraints in XPLOR-NIH
AuthorsZornetzer, G.A. / Fox, B.G. / Markley, J.L.
CitationJournal: Biochemistry / Year: 2006
Title: Solution structures of spinach acyl carrier protein with decanoate and stearate
Authors: Zornetzer, G.A. / Fox, B.G. / Markley, J.L.
History
DepositionJan 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of the protein has 100% match to the sequence from GB entry CAA31207 (ACP-I ...SEQUENCE The sequence of the protein has 100% match to the sequence from GB entry CAA31207 (ACP-I polypeptide, synthetic construct).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl Carrier Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3753
Polymers8,8451
Non-polymers5312
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 / 200structures with lowest energy in a clustering of the fatty acid structures
RepresentativeModel #1lowest energy

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Components

#1: Protein Acyl Carrier Protein /


Mass: 8844.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Plasmid: pSACP-2t / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07854
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical ChemComp-DKA / DECANOIC ACID / Capric acid


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131f1 filtered NOESY-15N HSQC
141f1 filtered NOESY-13C HSQC

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Sample preparation

DetailsContents: 2 mM protein, 10 mM MES pH 6.1, 100 mM NaCl, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.1 / Pressure: 1 atm / Temperature: 287 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionClassification
XwinNMR2.6collection
NMRPipedata analysis
Sparky3.111data analysis
CYANA2.1structure solution
XPLOR-NIH2.12refinement
RefinementMethod: Initial structure from torsion angle dynamics (in CYANA). Fatty acid, phosphopantetheine were added, docked using ambiguous distance restraints in XPLOR-NIH
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with lowest energy in a clustering of the fatty acid structures
Conformers calculated total number: 200 / Conformers submitted total number: 20

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