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- PDB-6ghh: Thermodynamic, Crystallographic and Computational Studies of Non ... -

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Basic information

Entry
Database: PDB / ID: 6ghh
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 / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-TRIDECANOIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionMay 7, 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 1.2Jan 17, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)18,5162
Polymers18,3011
Non-polymers2141
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-8 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.588, 53.588, 111.607
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 (cattle) / Gene: LGB / Production host: Bos taurus (cattle) / Tissue (production host): milk / References: UniProt: P02754
#2: Chemical ChemComp-TDA / N-TRIDECANOIC ACID


Mass: 214.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.495 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 7.3
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: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→13.8 Å / Num. obs: 17826 / % possible obs: 99.7 % / Redundancy: 4.5 % / Net I/σ(I): 8.2
Reflection shellResolution: 1.9→2.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GX9

1gx9


Resolution: 1.9→13.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.441 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24751 625 4.1 %RANDOM
Rwork0.19709 ---
obs0.1992 14552 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 45.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.9→13.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 15 76 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141332
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171282
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.6661804
X-RAY DIFFRACTIONr_angle_other_deg0.9641.6633018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08225.76359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53215256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.773153
X-RAY DIFFRACTIONr_chiral_restr0.0880.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
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_it2.4892.188653
X-RAY DIFFRACTIONr_mcbond_other2.492.187652
X-RAY DIFFRACTIONr_mcangle_it4.1523.266816
X-RAY DIFFRACTIONr_mcangle_other4.153.266817
X-RAY DIFFRACTIONr_scbond_it2.7772.543679
X-RAY DIFFRACTIONr_scbond_other2.7752.544680
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4793.665988
X-RAY DIFFRACTIONr_long_range_B_refined8.0741.6445361
X-RAY DIFFRACTIONr_long_range_B_other7.99441.3385321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 45 -
Rwork0.297 1019 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 42.399 Å / Origin y: -50.112 Å / Origin z: 114.966 Å
111213212223313233
T0.2007 Å2-0.1051 Å20.0051 Å2-0.1092 Å2-0.0163 Å2--0.0156 Å2
L2.0724 °20.7835 °2-1.2013 °2-4.5531 °2-1.1732 °2--6.3065 °2
S-0.298 Å °0.2596 Å °0.0937 Å °-0.3248 Å °0.1812 Å °0.0494 Å °-0.0526 Å °-0.5016 Å °0.1169 Å °

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