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Basic information

Entry
Database: PDB / ID: 6ge7
TitleThermodynamic, Crystallographic and Computational Studies of Non Mammalian Fatty Acid Binding to Bovine b-Lactoglobulin
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / fatty acid / Non-Mammalian
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
nonadecanoic acid / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsKontopidis, G. / Rovoli, M.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Thermodynamic, crystallographic and computational studies of non-mammalian fatty acid binding to bovine beta-Lactoglobulin.
Authors: Rovoli, M. / Thireou, T. / Choiset, Y. / Haertle, T. / Sawyer, L. / Eliopoulos, E. / Kontopidis, G.
History
DepositionApr 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6002
Polymers18,3011
Non-polymers2991
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.999, 53.999, 111.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18301.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Production host: Bos taurus (domestic cattle) / Tissue (production host): milk / References: UniProt: P02754
#2: Chemical ChemComp-EW8 / nonadecanoic acid


Mass: 298.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein 20 mg/mL, ligand 10mM, 20mM Tris buffer, pH 8, which were mixed with 4 microliter of well solution. Drops were equilibrated against 1 mL of well solution containing 1.43 M sodium ...Details: protein 20 mg/mL, ligand 10mM, 20mM Tris buffer, pH 8, which were mixed with 4 microliter of well solution. Drops were equilibrated against 1 mL of well solution containing 1.43 M sodium citrate and 0.1M Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 8916 / % possible obs: 98.9 % / Redundancy: 9.4 % / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 435

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DENZOdata reduction
SORTRFdata scaling
MOLREPphasing
RefinementResolution: 2.3→24.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.533 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.24 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24778 418 4.8 %RANDOM
Rwork0.19191 ---
obs0.19456 8317 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 47.083 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.14 Å20 Å2
2---0.27 Å2-0 Å2
3---0.88 Å2
Refinement stepCycle: 1 / Resolution: 2.3→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 21 77 1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0151350
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181313
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.7651826
X-RAY DIFFRACTIONr_angle_other_deg0.4991.7563097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0785169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75224.28642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49915229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.511153
X-RAY DIFFRACTIONr_chiral_restr0.0650.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02212
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_it2.0822.939655
X-RAY DIFFRACTIONr_mcbond_other2.082.94656
X-RAY DIFFRACTIONr_mcangle_it3.5274.402819
X-RAY DIFFRACTIONr_mcangle_other3.5254.402820
X-RAY DIFFRACTIONr_scbond_it2.063.194693
X-RAY DIFFRACTIONr_scbond_other2.0593.193694
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.464.6841003
X-RAY DIFFRACTIONr_long_range_B_refined6.2336.4311372
X-RAY DIFFRACTIONr_long_range_B_other6.11436.3331365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 30 -
Rwork0.3 595 -
obs--96.15 %
Refinement TLS params.Method: refined / Origin x: 11.168 Å / Origin y: 50.553 Å / Origin z: 59.371 Å
111213212223313233
T0.1161 Å2-0.0507 Å20.0229 Å2-0.0716 Å2-0.0131 Å2--0.0233 Å2
L2.4021 °20.7675 °21.1453 °2-3.0851 °2-0.0156 °2--4.9355 °2
S-0.2174 Å °0.3032 Å °-0.1764 Å °-0.262 Å °0.1625 Å °-0.1798 Å °0.1485 Å °0.3864 Å °0.0549 Å °

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