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- PDB-1sa8: THE NMR STRUCTURE OF A STABLE AND COMPACT ALL-beta-SHEET VARIANT ... -

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Basic information

Entry
Database: PDB / ID: 1sa8
TitleTHE NMR STRUCTURE OF A STABLE AND COMPACT ALL-beta-SHEET VARIANT OF INTESTINAL FATTY ACID-BINDING PROTEIN
ComponentsFatty acid-binding protein, intestinal
KeywordsLIPID BINDING PROTEIN / Intestinal fatty acid-binding protein / Protein stability / protein structure
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 / ARIA1.1.2, CNS1.1
AuthorsOgbay, B. / DeKoster, G.T. / Cistola, D.P.
CitationJournal: Protein Sci. / Year: 2004
Title: The NMR structure of a stable and compact all-beta-sheet variant of intestinal fatty acid-binding protein.
Authors: Ogbay, B. / Dekoster, G.T. / Cistola, D.P.
History
DepositionFeb 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE THE PROTEIN IS A DELETION MUTANT WHERE 27 CONSECUTIVE RESIDUES WERE DELETED FOR WILD-TYPE ...SEQUENCE THE PROTEIN IS A DELETION MUTANT WHERE 27 CONSECUTIVE RESIDUES WERE DELETED FOR WILD-TYPE INTESTINAL FATTY-ACID BINDING PROTEIN (I-FABP), AND REPLACED BY A GLY-GLY LINKER (GLY 9A - GLY 10A).

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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)11,9031
Polymers11,9031
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11903.436 Da / Num. of mol.: 1 / Fragment: D27-GG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FABP2 / Plasmid: PMON5840-IFABP(DELTA17SG) / Species (production host): Escherichia coli / Cell (production host): small intestinal enterocyte / Cellular location (production host): cytoplasm
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain (production host): MG1655 / Keywords: deletion of helica domain from I-FABP / References: UniProt: P02693

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-edited NOESY-HSQC
12115N-edited NOESY-HSQC
1313D 15N-15N edited NOESY
141Aromatic13C-NOESY-HSQC

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Sample preparation

DetailsContents: 1.8 mM protein, 20 mM potassium phosphate, 135 mM KCl, 10 mM NaCl, 0.5% NaN3,95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM potassium phosphate, 135 mM KCl, 10 mM NaCl, 0.5% NaN3
pH: 7.2 / Pressure: atmospheric atm / 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 UNITYVarianUNITY5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1NILGES, M. AND O'DONOGHUE, S. (1998) PROG. NMR SPECTROSCOPY 32, 107-139.2. LINGE, J. AND NILGES, M. (1999) JOURNAL OF BIOMOLECULAR NMR 13, 51-59.structure solution
Felix2001Accelrys Inc.data analysis
VNMR6.1Varian Associatescollection
CNS1.1NILGES, M. AND O'DONOGHUE, S. (1998) PROG. NMR SPECTROSCOPY 32, 107-139.2. LINGE, J. AND NILGES, M. (1999) JOURNAL OF BIOMOLECULAR NMR 13, 51-59.refinement
RefinementMethod: ARIA1.1.2, CNS1.1 / Software ordinal: 1
Details: The structures are based on a total of 2173 distance constraints and 176 CSI-derived 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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