[English] 日本語
Yorodumi
- PDB-1ael: NMR STRUCTURE OF APO INTESTINAL FATTY ACID-BINDING PROTEIN, 20 ST... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ael
TitleNMR STRUCTURE OF APO INTESTINAL FATTY ACID-BINDING PROTEIN, 20 STRUCTURES
ComponentsFATTY ACID-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / FATTY ACID-BINDING PROTEIN / LIPID TRANSPORT / I-FABP / LIPID-BINDING PROTEIN
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 / SIMULATED ANNEALING REFINEMENT
AuthorsHodsdon, M.E. / Cistola, D.P.
Citation
Journal: Biochemistry / Year: 1997
Title: Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange.
Authors: Hodsdon, M.E. / Cistola, D.P.
#1: 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.
#2: Journal: Adv.Protein Chem. / Year: 1993
Title: Lipid Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins
Authors: Banaszak, L. / Winter, N. / Xu, Z. / Bernlohr, D.A. / Cowan, S. / Jones, T.A.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: Rat Intestinal Fatty Acid Binding Protein. A Model System for Analyzing the Forces that Can Bind Fatty Acids to Proteins
Authors: Sacchettini, J.C. / Gordon, J.I.
#4: Journal: J.Biol.Chem. / Year: 1992
Title: Refinement of the Structure of Recombinant Rat Intestinal Fatty Acid-Binding Apoprotein at 1.2-A Resolution
Authors: Scapin, G. / Gordon, J.I. / Sacchettini, J.C.
History
DepositionJul 30, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
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_keywords.text
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FATTY ACID-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0151
Polymers15,0151
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)20 / 21FINAL PENALTY FUNCTION VALUES LESS THAN 10.0
Representative

-
Components

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


Mass: 15015.015 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INTESTINAL / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: SMALL INTESTINAL ENTEROCYTE / Plasmid: PMON5840-I-FABP / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain (production host): MG1655 / References: UniProt: P02693

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2-D 1H-HOMONUCLEAR NOESY
NMR detailsText: LIMITS ON SECONDARY STRUCTURE ELEMENTS WERE DEFINED BY THE PROTON-CARBON CONSENSUS CHEMICAL SHIFT INDEX.

-
Sample preparation

Sample conditionspH: 7.2 / Temperature: 306 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
TinkerPONDERrefinement
Tinkerstructure solution
RefinementMethod: SIMULATED ANNEALING REFINEMENT / Software ordinal: 1
NMR ensembleConformer selection criteria: FINAL PENALTY FUNCTION VALUES LESS THAN 10.0
Conformers calculated total number: 21 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more