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- PDB-5gge: Fatty Acid-Binding Protein in Brain Tissue of Drosophila melanogaster -

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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, isoform B
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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