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- PDB-4ib9: Bovine beta-lactoglobulin (isoform B) in complex with dodecyltrim... -

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Basic information

Entry
Database: PDB / ID: 4ib9
TitleBovine beta-lactoglobulin (isoform B) in complex with dodecyltrimethylammonium (DTAC)
Componentsbeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lipocalin
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
DODECANE-TRIMETHYLAMINE / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLoch, J.I. / Bonarek, P. / Polit, A. / Swiatek, S. / Dziedzicka-Wasylewska, M. / Lewinski, K.
CitationJournal: J.Mol.Recognit. / Year: 2013
Title: The differences in binding 12-carbon aliphatic ligands by bovine beta-lactoglobulin isoform A and B studied by isothermal titration calorimetry and X-ray crystallography
Authors: Loch, J.I. / Bonarek, P. / Polit, A. / Swiatek, S. / Dziedzicka-Wasylewska, M. / Lewinski, K.
History
DepositionDec 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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)18,6223
Polymers18,3011
Non-polymers3212
Water64936
1
A: beta-lactoglobulin
hetero molecules

A: beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2436
Polymers36,6022
Non-polymers6414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
2
A: beta-lactoglobulin
hetero molecules

A: beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2436
Polymers36,6022
Non-polymers6414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1740 Å2
ΔGint-7 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.030, 53.030, 109.320
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 (cattle) / References: UniProt: P02754
#2: Chemical ChemComp-CAT / DODECANE-TRIMETHYLAMINE


Mass: 228.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H34N
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.34M TRISODIUM CITRATE, 0.1M 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: Feb 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→13.36 Å / Num. all: 9497 / Num. obs: 9317 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1263 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
REFMAC5.6.0117refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.2→13.36 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.88 / SU B: 6.22 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30643 908 9.8 %RANDOM
Rwork0.2451 ---
obs0.25106 8383 97.73 %-
all-9291 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.935 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→13.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 22 36 1322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021312
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.0061772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60926.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.99415251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.248153
X-RAY DIFFRACTIONr_chiral_restr0.0920.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021935
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 46 -
Rwork0.185 498 -
obs--91.89 %

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