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- PDB-1t8v: The NMR structure of d34a i-fabp: implications for the determinan... -

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Basic information

Entry
Database: PDB / ID: 1t8v
TitleThe NMR structure of d34a i-fabp: implications for the determinants of ligand binding stoichiometry
ComponentsFatty acid-binding protein, intestinal
KeywordsLIPID BINDING PROTEIN / fatty acid / stoichiometry
Function / homology
Function and homology information


Triglyceride catabolism / intestinal lipid absorption / apical cortex / intestinal absorption / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / microvillus / long-chain fatty acid transport / fatty acid transport / fatty acid binding ...Triglyceride catabolism / intestinal lipid absorption / apical cortex / intestinal absorption / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / microvillus / long-chain fatty acid transport / fatty acid transport / fatty acid binding / fatty acid metabolic process / nucleus / cytosol
Similarity search - Function
Fatty acid-binding protein, intestinal / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, intestinal
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsOgbay, B. / Cistola, D.P.
Citation
Journal: To be published
Title: THE NMR STRUCTURE OF D34A I-FABP: IMPLICATIONS FOR THE DETERMINANTS OF LIGAND BINDING STOICHIOMETRY
Authors: Ogbay, B. / Cistola, D.P.
#1: Journal: Protein Sci. / Year: 2004
Title: The NMR structure of a stable and compact all-B-sheet variant of intestinal fatty acid-binding protein
Authors: Cistola, D.P. / Ogbay, B. / Dekoster, G.T.
History
DepositionMay 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Fatty acid-binding protein, intestinal


Theoretical massNumber of molelcules
Total (without water)14,9711
Polymers14,9711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fatty acid-binding protein, intestinal / I-FABP / D34A I-FABP / FABPI


Mass: 14971.005 Da / Num. of mol.: 1 / Mutation: D34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FABP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02693

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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
1313D 13C AROMATIC NOESY
1413D 15N-15N NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 20 mM potassium phosphate, 50 mM KCl, 0.5% NaN3, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 50mM KCl / pH: 7.2 / Temperature: 298 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
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Associatescollection
Felix2001Accelrys Inc.processing
CNS1.1Brnger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, T. J., Rice, L. M., Simonson, T., and Warren, G. Lstructure solution
ARIA1.2Linge, O'Donoghue, Nilgesstructure solution
ARIA1.2Linge, O'Donoghue, Nilgesrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 3471 NOE-derived restraints and 80 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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