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- PDB-5bvq: Ligand-unbound pFABP4 -

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Basic information

Entry
Database: PDB / ID: 5bvq
TitleLigand-unbound pFABP4
Componentsfatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / Fatty acid-binding protein / beta-barrel protein / Gentoo penguin (Pygoscelis papua)
Function / homology
Function and homology information


cellular response to linoleic acid / stearic acid binding / linoleic acid binding / oleic acid binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid transport / 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
Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesPygoscelis papua (Gentoo penguin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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: fatty acid-binding protein
B: fatty acid-binding protein


Theoretical massNumber of molelcules
Total (without water)29,9262
Polymers29,9262
Non-polymers00
Water1,946108
1
A: fatty acid-binding protein


Theoretical massNumber of molelcules
Total (without water)14,9631
Polymers14,9631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fatty acid-binding protein


Theoretical massNumber of molelcules
Total (without water)14,9631
Polymers14,9631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.001, 61.001, 143.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein fatty acid-binding protein /


Mass: 14962.997 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pygoscelis papua (Gentoo penguin) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0MJN3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Tris (pH 8.3), 27% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 17556 / % possible obs: 99.3 % / Redundancy: 21.9 % / Net I/σ(I): 87.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
RefinementResolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.578 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29624 852 4.9 %RANDOM
Rwork0.24004 ---
obs0.24291 16639 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.412 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 0 108 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022118
X-RAY DIFFRACTIONr_bond_other_d0.0010.022046
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.9462850
X-RAY DIFFRACTIONr_angle_other_deg0.87534714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6995262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5925.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5415410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3771512
X-RAY DIFFRACTIONr_chiral_restr0.110.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
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_it3.7633.8861054
X-RAY DIFFRACTIONr_mcbond_other3.7213.8821053
X-RAY DIFFRACTIONr_mcangle_it5.295.8141314
X-RAY DIFFRACTIONr_mcangle_other5.2975.8171315
X-RAY DIFFRACTIONr_scbond_it4.3234.3341064
X-RAY DIFFRACTIONr_scbond_other4.3194.3321064
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7066.2891536
X-RAY DIFFRACTIONr_long_range_B_refined8.97731.2912388
X-RAY DIFFRACTIONr_long_range_B_other8.96531.1452367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 64 -
Rwork0.291 1233 -
obs--100 %

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