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- PDB-3uex: Bovine beta-lactoglobulin complex with stearic acid -

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Basic information

Entry
Database: PDB / ID: 3uex
TitleBovine beta-lactoglobulin complex with stearic acid
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / beta protein / beta barrel / lipocalin / bovine milk
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ETHANOL / STEARIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLoch, J. / Lewinski, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2012
Title: Bovine beta-lactoglobulin complex with stearic 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 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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
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)18,7245
Polymers18,3011
Non-polymers4234
Water81145
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,44810
Polymers36,6022
Non-polymers8458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.778, 53.778, 112.038
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 (cattle) / References: UniProt: P02754
#2: Chemical ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#3: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.87 %
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 239K, 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: Jan 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.897
11h+k,-k,-l20.103
ReflectionResolution: 2.1→15 Å / Num. all: 11456 / Num. obs: 11250 / % possible obs: 98.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2 / Num. unique all: 1575 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CrysalisProPROdata collection
MOLREPphasing
REFMAC5.5.0102refinement
CrysalisProPROdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1BSY

1bsy


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.88 / SU B: 4.372 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28366 1124 10 %RANDOM
Rwork0.22997 ---
obs0.2353 10104 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.531 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2--2.25 Å20 Å2
3----4.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 29 45 1334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221331
X-RAY DIFFRACTIONr_angle_refined_deg1.5922.0081796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0925165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84626.78656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.55515255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.588153
X-RAY DIFFRACTIONr_chiral_restr0.10.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021951
X-RAY DIFFRACTIONr_mcbond_it0.9281.5813
X-RAY DIFFRACTIONr_mcangle_it1.64121320
X-RAY DIFFRACTIONr_scbond_it2.0863518
X-RAY DIFFRACTIONr_scangle_it3.3614.5472
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 77 -
Rwork0.236 706 -
obs--92.88 %

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