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- PDB-1nti: RDC-refined NMR structure of bovine Acyl-coenzyme A Binding Prote... -

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Basic information

Entry
Database: PDB / ID: 1nti
TitleRDC-refined NMR structure of bovine Acyl-coenzyme A Binding Protein, ACBP
ComponentsAcyl-CoA-binding protein
KeywordsLIPID BINDING PROTEIN / four-helix-bundle / ACBP family
Function / homology
Function and homology information


Mitochondrial Fatty Acid Beta-Oxidation / fatty-acyl-CoA binding / fatty acid metabolic process / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / FERM/acyl-CoA-binding protein superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl-CoA-binding protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsLerche, M.H. / Kragelund, B.B. / Redfield, C. / Poulsen, F.M.
Citation
Journal: To be Published
Title: Subtle structural response to ligand binding revealed by residual dipolar coupling refined NMR structures of acyl coenzyme A binding protein
Authors: Lerche, M.H. / Kragelund, B.B. / Redfield, C. / Poulsen, F.M.
#1: Journal: J.Biomol.NMR / Year: 1993
Title: The three-dimensional structure of acyl-coenzyme A binding protein from bovine liver: structural refinement using heteronuclear multidimensional NMR spectroscopy.
Authors: Andersen, K.V. / Poulsen, F.M.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Three-dimensional structure of the complex between acyl-coenzyme A binding protein and palmitoyl-coenzyme A.
Authors: Kragelund, B.B. / Andersen, K.V. / Madsen, J.C. / Knudsen, J. / Poulsen, F.M.
History
DepositionJan 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9311
Polymers9,9311
Non-polymers00
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 #19lowest energy

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Components

#1: Protein Acyl-CoA-binding protein / ACBP


Mass: 9931.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P07107

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111S3E
1213D 15N-separated NOESY
NMR detailsText: refinement of earlier pdb deposit, 2ABD, see entry for detail. NOE and dihedral angle constraints obtained from this entry. Residual dipolar couplings added as additional restraints

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM recombinant bovine ACBP, 5% 3:1 [DMPC:DHPC], pH 6.510% D2O, 90% H2O
20.5mM recombinant bovine ACBP, pH 6.510% D2O, 90% H2O
Sample conditionsIonic strength: no salt added / pH: 6.5 / Pressure: ambient / Temperature: 310 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 AMXBrukerAMX6001
Home-built homebuiltHome-builthomebuilt6002

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Processing

NMR softwareName: X-PLOR / Version: modified 3.8 / Classification: refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
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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