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- PDB-1a57: THE THREE-DIMENSIONAL STRUCTURE OF A HELIX-LESS VARIANT OF INTEST... -

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Entry
Database: PDB / ID: 1a57
TitleTHE THREE-DIMENSIONAL STRUCTURE OF A HELIX-LESS VARIANT OF INTESTINAL FATTY ACID BINDING PROTEIN, NMR, 20 STRUCTURES
ComponentsINTESTINAL FATTY ACID-BINDING PROTEIN
KeywordsFATTY ACID-BINDING / LIPID TRANSPORT / BETA-CLAM / LIPOCALINS
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 WITH SIMULATED ANNEALING REFINEMENT
AuthorsSteele, R.A. / Emmert, D.A. / Kao, J. / Hodsdon, M.E. / Frieden, C. / Cistola, D.P.
Citation
Journal: Protein Sci. / Year: 1998
Title: The three-dimensional structure of a helix-less variant of intestinal fatty acid-binding protein.
Authors: Steele, R.A. / Emmert, D.A. / Kao, J. / Hodsdon, M.E. / Frieden, C. / Cistola, D.P.
#1: Journal: Biochemistry / Year: 1997
Title: Discrete Backbone Disorder in the Nuclear Magnetic Resonance Structure of Apo Intestinal Fatty Acid-Binding Protein: Implications for the Mechanism of Ligand Entry
Authors: Hodsdon, M.E. / Cistola, D.P.
#2: Journal: Biochemistry / Year: 1996
Title: Fatty Acid Interactions with a Helix-Less Variant of Intestinal Fatty Acid-Binding Protein
Authors: Cistola, D.P. / Kim, K. / Rogl, H. / Frieden, C.
#3: Journal: Biochemistry / Year: 1996
Title: Intestinal Fatty Acid-Binding Protein: The Structure and Stability of a Helix-Less Variant
Authors: Kim, K. / Cistola, D.P. / Frieden, C.
#4: Journal: J.Mol.Biol. / Year: 1996
Title: The NMR Solution Structure of Intestinal Fatty Acid-Binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm
Authors: Hodsdon, M.E. / Ponder, J.W. / Cistola, D.P.
History
DepositionFeb 20, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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: INTESTINAL FATTY ACID-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,1651
Polymers13,1651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 23FINAL PENALTY FUNCTION VALUES GREATER THAN 10.0 OR GREATER THAN TWO STANDARD DEVIATIONS FROM THE MEAN WERE OMITTED
Representative

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Components

#1: Protein INTESTINAL FATTY ACID-BINDING PROTEIN / DELTA17SG / IFABP / I-FABP


Mass: 13164.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HELIX-LESS, COMPLEXED WITH PALMITATE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: SEE REMARK 1, REFERENCE 3 / Cell: SMALL INTESTINAL ENTEROCYTE / Cellular location: CYTOPLASM / Plasmid: PMON5840-IFABP(DELTA17SG) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain (production host): MG1655 / References: UniProt: P02693

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113-D 13C-RESOLVED NOESY
1213-D 15N-RESOLVED NOESY
1312-D 1H-HOMONUCLEAR NOESY
1412-D 13C-EDITED NOESY

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Sample preparation

Sample conditionspH: 7.2 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
TinkerPONDERrefinement
Tinkerstructure solution
RefinementMethod: DISTANCE GEOMETRY WITH SIMULATED ANNEALING REFINEMENT
Software ordinal: 1
Details: DISTANCE GEOMETRY WAS PERFORMED USING 5% PAIRWISE METRIZATION AND A GAUSSIAN TRIAL DISTRIBUTION FOR THE SELECTION OF DISTANCES USING THE PROGRAM DISTGEOM, A COMPONENT OF THE TINKER MOLECULAR ...Details: DISTANCE GEOMETRY WAS PERFORMED USING 5% PAIRWISE METRIZATION AND A GAUSSIAN TRIAL DISTRIBUTION FOR THE SELECTION OF DISTANCES USING THE PROGRAM DISTGEOM, A COMPONENT OF THE TINKER MOLECULAR MODELING PACKAGE. EMBEDDED STRUCTURES WERE REFINED VERSUS A PENALTY FUNCTION BASED SOLELY ON THE EXPERIMENTAL RESTRAINTS AND LOCAL COVALENT GEOMETRY (BOND LENGTHS, ANGLES, CHIRALITY); NO ENERGY-BASED TERMS WERE INCLUDED. DETAILS OF THE CALCULATIONS AND STRUCTURAL STATISTICS ARE GIVEN IN THE PAPER CITED ON THE JRNL RECORDS ABOVE. THE LOOP FROM RESIDUES 8 - 20 IS ENTIRELY UNRESTRAINED. THIS REGION CONTAINS THE SITE OF THE DELETED HELICES OF I-FABP. CARE SHOULD BE TAKEN WHEN ANALYZING STATISTICS ON THIS MOLECULE AS THIS UNRESTRAINED LOOP WILL ABNORMALLY SKEW ANY RESULTS.
NMR ensembleConformer selection criteria: FINAL PENALTY FUNCTION VALUES GREATER THAN 10.0 OR GREATER THAN TWO STANDARD DEVIATIONS FROM THE MEAN WERE OMITTED
Conformers calculated total number: 23 / Conformers submitted total number: 20

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