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Yorodumi- PDB-1a57: THE THREE-DIMENSIONAL STRUCTURE OF A HELIX-LESS VARIANT OF INTEST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a57 | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF A HELIX-LESS VARIANT OF INTESTINAL FATTY ACID BINDING PROTEIN, NMR, 20 STRUCTURES | ||||||
Components | INTESTINAL FATTY ACID-BINDING PROTEIN | ||||||
Keywords | FATTY 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 metabolic process ...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 metabolic process / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY WITH SIMULATED ANNEALING REFINEMENT | ||||||
Authors | Steele, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a57.cif.gz | 730.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a57.ent.gz | 615.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a57 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a57 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 7.2 / Temperature: 298 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: 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 ensemble | Conformer 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 |