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- PDB-2cqu: Solution Structure of RSGI RUH-045, a Human Acyl-CoA Binding Protein -

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Basic information

Entry
Database: PDB / ID: 2cqu
TitleSolution Structure of RSGI RUH-045, a Human Acyl-CoA Binding Protein
Componentsperoxisomal D3,D2-enoyl-CoA isomerase
KeywordsISOMERASE / Acyl-CoA binding protein / Homo sapiens / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle ...Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle / mitochondrion / membrane / cytosol
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 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase ...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 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / FERM/acyl-CoA-binding protein superfamily / ClpP/crotonase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Enoyl-CoA delta isomerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsTsubota, Y. / Ruhul Momen, A.Z.M. / Onuki, H. / Hirota, H. / Saito, K. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of RSGI RUH-045, a Human Acyl-CoA Binding Protein
Authors: Tsubota, Y. / Ruhul Momen, A.Z.M. / Onuki, H. / Hirota, H. / Saito, K. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peroxisomal D3,D2-enoyl-CoA isomerase


Theoretical massNumber of molelcules
Total (without water)12,4371
Polymers12,4371
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 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein peroxisomal D3,D2-enoyl-CoA isomerase / RSGI RUH-045 / Acyl-CoA Binding Protein


Mass: 12436.909 Da / Num. of mol.: 1 / Fragment: ACBP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis (E.coli) / Plasmid: P040329-47
References: UniProt: O75521, Delta3-Delta2-enoyl-CoA isomerase

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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

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Sample preparation

DetailsContents: 0.60mM Acyl-CoA binding protein U-15N, 13C; 20mM d-Tris-HCl(pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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