[English] 日本語
Yorodumi
- PDB-5gge: Fatty Acid-Binding Protein in Brain Tissue of Drosophila melanogaster -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gge
TitleFatty Acid-Binding Protein in Brain Tissue of Drosophila melanogaster
ComponentsFatty acid bindin protein, isoform B
KeywordsLIPID BINDING PROTEIN / Fatty Acid Binding Protein
Function / homology
Function and homology information


long-term memory / fatty acid transport / fatty acid binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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
CITRIC ACID / Fatty acid-binding protein, muscle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.861 Å
AuthorsCheng, Y.-Y. / Huang, Y.-F. / Lin, H.-H. / Chang, W.W. / Lyu, P.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology, R.O.C.103-2311-B-007-007-MY2 Taiwan
Citation
Journal: Biochim Biophys Acta Mol Cell Biol Lipids / Year: 2019
Title: The ligand-mediated affinity of brain-type fatty acid-binding protein for membranes determines the directionality of lipophilic cargo transport.
Authors: Cheng, Y.-Y. / Huang, Y.-F. / Lin, H.-H. / Chang, W.W. / Lyu, P.-C.
#1: Journal: To Be Published
Title: Revisit the Relationship of Thermal Stability and Purity in Recombinant Drosophila Fatty Acid-Binding protein
Authors: Cheng, Y.-Y. / Huang, Y.-F. / Lin, H.-H.
History
DepositionJun 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid bindin protein, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7132
Polymers14,5211
Non-polymers1921
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint2 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.698, 61.698, 137.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Fatty acid bindin protein, isoform B / RH06221p / RH49003p


Mass: 14520.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: fabp, CG6783, Dmel_CG6783 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9VGM2
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 2M ammonia sulfate, 100mM phosphate citrate, pH4.2

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 11582 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 11.5
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.96 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data processing
SCALEPACKdata reduction
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTP

1ftp


Resolution: 1.861→27.052 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9
RfactorNum. reflection% reflection
Rfree0.2458 1152 10 %
Rwork0.1789 --
obs0.1855 11518 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.861→27.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 13 139 1160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121044
X-RAY DIFFRACTIONf_angle_d1.2971402
X-RAY DIFFRACTIONf_dihedral_angle_d15.881399
X-RAY DIFFRACTIONf_chiral_restr0.055168
X-RAY DIFFRACTIONf_plane_restr0.006174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8605-1.94520.26481400.22081269X-RAY DIFFRACTION99
1.9452-2.04770.27961400.20241250X-RAY DIFFRACTION99
2.0477-2.17590.3081410.19041272X-RAY DIFFRACTION100
2.1759-2.34380.25981420.18421274X-RAY DIFFRACTION100
2.3438-2.57960.23041430.18621287X-RAY DIFFRACTION100
2.5796-2.95240.24311440.18771299X-RAY DIFFRACTION100
2.9524-3.71820.22151460.16111317X-RAY DIFFRACTION100
3.7182-27.05430.24371560.16991398X-RAY DIFFRACTION99

+
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