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- PDB-5bvt: Palmitate-bound pFABP5 -

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Basic information

Entry
Database: PDB / ID: 5bvt
TitlePalmitate-bound pFABP5
ComponentsEpidermal fatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / Fatty acid-binding protein / beta-barrel protein / Gentoo penguin (Pygoscelis papua)
Function / homology
Function and homology information


postsynaptic density / lipid binding / extracellular region / nucleus / cytoplasm
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
PALMITOLEIC ACID / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesPygoscelis papua (Gentoo penguin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å
AuthorsLee, J.H. / Lee, C.W. / Do, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin
Authors: Lee, C.W. / Kim, J.E. / Do, H. / Kim, R.O. / Lee, S.G. / Park, H.H. / Chang, J.H. / Yim, J.H. / Park, H. / Kim, I.C. / Lee, J.H.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epidermal fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3822
Polymers15,1271
Non-polymers2541
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint3 kcal/mol
Surface area6890 Å2
Unit cell
Length a, b, c (Å)29.497, 60.250, 35.732
Angle α, β, γ (deg.)90.00, 113.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epidermal fatty acid-binding protein


Mass: 15127.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pygoscelis papua (Gentoo penguin) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0MJ13*PLUS
#2: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 1.93 Å3/Da / Density % sol: 36.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M Tris (pH 8.5), 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 4997 / % possible obs: 97.6 % / Redundancy: 7.5 % / Net I/σ(I): 61.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
Cootmodel building
RefinementResolution: 2.31→32.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.873 / SU B: 9.157 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.865 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26912 231 4.6 %RANDOM
Rwork0.17038 ---
obs0.175 4753 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.04 Å2
2---0.03 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.31→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 18 56 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021083
X-RAY DIFFRACTIONr_bond_other_d0.0010.021078
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9861441
X-RAY DIFFRACTIONr_angle_other_deg0.73832503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26925.68244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64415221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.527154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0732.952535
X-RAY DIFFRACTIONr_mcbond_other2.0712.949534
X-RAY DIFFRACTIONr_mcangle_it3.3224.418667
X-RAY DIFFRACTIONr_mcangle_other3.324.421668
X-RAY DIFFRACTIONr_scbond_it2.8473.329548
X-RAY DIFFRACTIONr_scbond_other2.8453.332549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7034.809775
X-RAY DIFFRACTIONr_long_range_B_refined6.58523.1231184
X-RAY DIFFRACTIONr_long_range_B_other6.57823.1321179
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.309→2.368 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 15 -
Rwork0.23 323 -
obs--91.6 %

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