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- PDB-4dq4: Bovine beta-lactoglobulin complex with linoleic acid -

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Basic information

Entry
Database: PDB / ID: 4dq4
TitleBovine beta-lactoglobulin complex with linoleic acid
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lipocalin / bovine milk
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
LINOLEIC ACID / ETHANOL / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLoch, J.I. / Lewinski, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2013
Title: Binding of 18-carbon unsaturated fatty acids to bovine beta-lactoglobulin--structural and thermodynamic studies.
Authors: Loch, J.I. / Bonarek, P. / Polit, A. / Ries, D. / Dziedzicka-Wasylewska, M. / Lewinski, K.
History
DepositionFeb 15, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 29, 2012ID: 3QZK
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: 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 1.4Nov 6, 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)18,7204
Polymers18,3011
Non-polymers4193
Water1,67593
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4408
Polymers36,6022
Non-polymers8376
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 software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.33, 53.33, 111.53
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 / Fragment: UNP residues 17-178 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02754
#2: Chemical ChemComp-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID


Mass: 280.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl buffer, 1.34M tri-sodium citrate, 1mM linoleic acid in ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→13.35 Å / Num. all: 11259 / Num. obs: 11101 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 3.8 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
REFMAC5.2.0005refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BSY

1bsy


Resolution: 2.1→13.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.864 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28966 1110 10 %RANDOM
Rwork0.22093 ---
obs0.22806 9948 98.86 %-
all-11186 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.577 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→13.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 29 93 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221366
X-RAY DIFFRACTIONr_bond_other_d0.0010.021290
X-RAY DIFFRACTIONr_angle_refined_deg1.3332.0111849
X-RAY DIFFRACTIONr_angle_other_deg0.79833043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.88526.84257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96315266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.386153
X-RAY DIFFRACTIONr_chiral_restr0.0770.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_nbd_refined0.1940.2298
X-RAY DIFFRACTIONr_nbd_other0.1810.21366
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2627
X-RAY DIFFRACTIONr_nbtor_other0.0840.2870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.215
X-RAY DIFFRACTIONr_mcbond_it1.1141.51081
X-RAY DIFFRACTIONr_mcbond_other0.1291.5330
X-RAY DIFFRACTIONr_mcangle_it1.25521358
X-RAY DIFFRACTIONr_scbond_it1.3973611
X-RAY DIFFRACTIONr_scangle_it2.0874.5487
LS refinement shellResolution: 2.102→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 80 -
Rwork0.254 688 -
obs--97.09 %

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