[English] 日本語
Yorodumi
- PDB-1fdq: CRYSTAL STRUCTURE OF HUMAN BRAIN FATTY ACID BINDING PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fdq
TitleCRYSTAL STRUCTURE OF HUMAN BRAIN FATTY ACID BINDING PROTEIN
ComponentsFATTY ACID-BINDING PROTEIN, BRAIN
KeywordsLIPID BINDING PROTEIN / OMEGA-3 / N-3 / LONG CHAIN POLY UNSATURATED FATTY ACID
Function / homology
Function and homology information


NOTCH3 Intracellular Domain Regulates Transcription / Triglyceride catabolism / fatty acid transport / epithelial cell proliferation / fatty acid binding / nervous system development / negative regulation of cell population proliferation / lipid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID / Fatty acid-binding protein, brain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBalendiran, G.K.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure and thermodynamic analysis of human brain fatty acid-binding protein.
Authors: Balendiran, G.K. / Schnutgen, F. / Scapin, G. / Borchers, T. / Xhong, N. / Lim, K. / Godbout, R. / Spener, F. / Sacchettini, J.C.
History
DepositionJul 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FATTY ACID-BINDING PROTEIN, BRAIN
B: FATTY ACID-BINDING PROTEIN, BRAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2104
Polymers29,5532
Non-polymers6572
Water1,72996
1
A: FATTY ACID-BINDING PROTEIN, BRAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1052
Polymers14,7771
Non-polymers3281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FATTY ACID-BINDING PROTEIN, BRAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1052
Polymers14,7771
Non-polymers3281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.22, 87.930, 46.790
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein FATTY ACID-BINDING PROTEIN, BRAIN / BRAIN LIPID BINDING PROTEIN


Mass: 14776.702 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15540
#2: Chemical ChemComp-HXA / DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID / Docosahexaenoic acid


Mass: 328.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 %PEG40001reservoir
30.1 MTris1reservoir
450 mM1reservoirNaOAc

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 21863 / % possible obs: 84.4 % / Redundancy: 5 % / Rsym value: 0.063
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Num. measured all: 102823 / Rmerge(I) obs: 0.063

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å
RfactorNum. reflection% reflection
Rfree0.257 --
Rwork0.18 --
all0.18 --
obs-21863 84.4 %
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 48 96 2218
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Rfactor all: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_angle_d2

+
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