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- PDB-5gkb: Crystal Structure of Fatty Acid-Binding Protein in Brain Tissue o... -

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Basic information

Entry
Database: PDB / ID: 5gkb
TitleCrystal Structure of Fatty Acid-Binding Protein in Brain Tissue of Drosophila melanogaster without citrate inside
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 / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid binding protein, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsCheng, Y.-Y. / Huang, Y.-F. / Lin, H.-H. / Chang, W.W. / Lyu, P.-C.
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
DepositionJul 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Nov 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


Theoretical massNumber of molelcules
Total (without water)14,5211
Polymers14,5211
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.595, 61.595, 137.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 0.1M phosphate citrate, 1.6M NaH2PO4, 0.4M K2HPO4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. obs: 8811 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 22.6
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 6.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGE

5gge


Resolution: 2.04→28.091 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.91
RfactorNum. reflection% reflection
Rfree0.2408 881 10 %
Rwork0.1858 --
obs0.1914 8811 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→28.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 128 1129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111012
X-RAY DIFFRACTIONf_angle_d1.2421363
X-RAY DIFFRACTIONf_dihedral_angle_d10.3859
X-RAY DIFFRACTIONf_chiral_restr0.066166
X-RAY DIFFRACTIONf_plane_restr0.009170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0393-2.1670.26491430.19191285X-RAY DIFFRACTION100
2.167-2.33420.23931430.17821290X-RAY DIFFRACTION100
2.3342-2.5690.27881440.1751296X-RAY DIFFRACTION100
2.569-2.94040.2431450.18061313X-RAY DIFFRACTION100
2.9404-3.70320.21091490.17181329X-RAY DIFFRACTION100
3.7032-28.09390.24281570.20471417X-RAY DIFFRACTION100

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