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- PDB-2m5r: Solution structure of holo-acyl carrier protein of Leishmania major -

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Basic information

Entry
Database: PDB / ID: 2m5r
TitleSolution structure of holo-acyl carrier protein of Leishmania major
ComponentsAcyl carrier protein
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


acyl binding / acyl carrier activity / fatty acid biosynthetic process / mitochondrial matrix / mitochondrion
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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
4'-PHOSPHOPANTETHEINE / Acyl carrier protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsKumar, A. / Surolia, A. / Sundd, M.
CitationJournal: To be Published
Title: NMR structures of the apo- and holo- forms of the acyl carrier protein of Leishmania major
Authors: Kumar, A. / Surolia, A. / Sundd, M.
History
DepositionMar 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: 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_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3642
Polymers9,0051
Non-polymers3581
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Acyl carrier protein


Mass: 9005.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: ACP, LMJF_27_0290 / Plasmid: pET 28 a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: E9AD06
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


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

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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 HN(CA)CB
1313D CBCA(CO)NH
1413D HNCA
1513D HNCO
1613D C(CO)NH
1713D 1H-15N TOCSY
1813D 1H-13C NOESY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 20 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 20 mM / Component: protein-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 100 / pH: 6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddardprocessing
CNSBrungerrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1956 / NOE intraresidue total count: 785 / NOE long range total count: 169 / NOE medium range total count: 398 / NOE sequential total count: 604 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 74
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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