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- PDB-1st7: Solution structure of Acyl Coenzyme A Binding Protein from yeast -

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Basic information

Entry
Database: PDB / ID: 1st7
TitleSolution structure of Acyl Coenzyme A Binding Protein from yeast
ComponentsAcyl-CoA-binding protein
KeywordsTRANSPORT PROTEIN / Four helix bundle
Function / homology
Function and homology information


very long-chain fatty acid biosynthetic process / long-chain fatty acyl-CoA binding / lipid binding / extracellular region / nucleus / cytosol / cytoplasm
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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Simulated annealing, CHARMM22 water refinement
AuthorsTeilum, K. / Thormann, T. / Caterer, N.R. / Poulsen, H.I. / Jensen, P.H. / Knudsen, J. / Kragelund, B.B. / Poulsen, F.M.
CitationJournal: Proteins / Year: 2005
Title: Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles
Authors: Teilum, K. / Thormann, T. / Caterer, N.R. / Poulsen, H.I. / Jensen, P.H. / Knudsen, J. / Kragelund, B.B. / Poulsen, F.M.
History
DepositionMar 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

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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)9,9431
Polymers9,9431
Non-polymers00
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 / 20structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9943.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ACB1, ACB, YGR037C / Plasmid: pETACBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLyS / References: UniProt: P31787

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 2.5 mM U-15N,13C / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.75 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8Brungerstructure solution
X-PLOR3.8Brungerrefinement
RefinementMethod: Simulated annealing, CHARMM22 water refinement / Software ordinal: 1
Details: The structure is based on 1040 NOE-derived distance constraints, 133 dihedral angle constraints, 13 distance constraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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