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

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Basic information

Entry
Database: PDB / ID: 1nvl
TitleRDC-refined NMR structure of bovine Acyl-coenzyme A Binding Protein, ACBP, in complex with palmitoyl-coenzyme A
ComponentsAcyl-CoA-binding protein
KeywordsLIGAND BINDING PROTEIN / 4-alpha-helix bundle / protein-ligand complex / palmitoyl-coenzyme A
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
COENZYME A / PALMITIC ACID / Acyl-CoA-binding protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS IN FULL CHARMM FORCE FIELD
AuthorsLerche, M.H. / Kragelund, B.B. / Redfield, C. / Poulsen, F.M.
Citation
Journal: To be Published / Year: 2003
Title: RDC-refined NMR structure of bovine Acyl-coenzyme A Binding Protein, ACBP, in complex with palmitoyl-coenzyme A
Authors: Lerche, M.H. / Kragelund, B.B. / Redfield, C. / Poulsen, F.M.
#1: 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.
#2: 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.
History
DepositionFeb 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2011Group: Derived calculations
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9553
Polymers9,9311
Non-polymers1,0242
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 #20lowest energy

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Components

#1: Protein Acyl-CoA-binding protein / ACBP / Diazepam binding inhibitor / DBI / Endozepine / EP


Mass: 9931.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ACBP / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07107
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121S3E-HSQC
NMR detailsText: REFINEMENT OF EARLIER PDB DEPOSIT, 1ACA, SEE ENTRY FOR DETAILS. NOE AND DIHEDRAL ANGLE CONSTRAINTS OBTAINED AND MODIFIED FROM THIS ENTRY. RESIDUAL DIPOLAR COUPLINGS ADDED AS ADDITIONAL RESTRAINTS.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM ACBP, pH 6.5, 0.5 mM palmitoyl-coenzyme A, 5% (3:1) [DMPC:DHPC], 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM ACBP, pH 6.5, 0.5 mM palmitoyl-coenzyme A, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1no salt added 6.5ambient 310 K
2no salt added 6.5ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Home-built home builtHome-builthome built6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORmodified 3.8Brnger, A. T.refinement
Pronto20000515Kjaer et al.data analysis
Felixprocessing
MNMRdata analysis
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS IN FULL CHARMM FORCE FIELD
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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