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- PDB-3ueu: Bovine beta-lactoglobulin complex with lauric acid -

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Basic information

Entry
Database: PDB / ID: 3ueu
TitleBovine beta-lactoglobulin complex with lauric acid
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / beta-barrel / beta protein / lipocalin / milk protein
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
LAURIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLREP / Resolution: 2.1 Å
AuthorsLoch, J. / Lewinski, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2012
Title: Bovine beta-lactoglobulin complex with lauric acid
Authors: Loch, J.I. / Polit, A. / Bonarek, P. / Olszewska, D. / Kurpiewska, K. / Dziedzicka-Wasylewska, M. / Lewinski, K.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650AUTHOR DETERMINED HELIX SECONDARY STRUCTURE RECORD

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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)18,5373
Polymers18,3011
Non-polymers2362
Water1,22568
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0746
Polymers36,6022
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area1400 Å2
ΔGint-21 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.870, 52.870, 110.503
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 natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.34 M trisodium citrarte, 0.1 Tris-HCl buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→11.38 Å / Num. all: 10953 / Num. obs: 10865 / % possible obs: 99.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 2.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
REFMAC5.2.0005refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLREP
Starting model: pdb entry 1BSY

1bsy


Resolution: 2.1→11.38 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.843 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25504 1084 10 %RANDOM
Rwork0.20945 ---
obs0.21412 9762 99.62 %-
all-10846 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.878 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→11.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 15 68 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221296
X-RAY DIFFRACTIONr_angle_refined_deg1.7642.0051758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4475165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11126.60453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72715255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.149153
X-RAY DIFFRACTIONr_chiral_restr0.1020.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02931
X-RAY DIFFRACTIONr_nbd_refined0.2230.2562
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.213
X-RAY DIFFRACTIONr_mcbond_it1.1171.5817
X-RAY DIFFRACTIONr_mcangle_it1.86421296
X-RAY DIFFRACTIONr_scbond_it2.3653540
X-RAY DIFFRACTIONr_scangle_it3.7594.5456
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 68 -
Rwork0.258 682 -
obs--98.94 %

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