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- PDB-4ib7: Bovine beta-lactoglobulin (isoform A) in complex with dodecyltrim... -

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Basic information

Entry
Database: PDB / ID: 4ib7
TitleBovine beta-lactoglobulin (isoform A) in complex with dodecyltrimethylammonium (DTAC)
Componentsbeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lipocalin
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
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, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)18,6162
Polymers18,3871
Non-polymers2281
Water55831
1
A: beta-lactoglobulin
hetero molecules

A: beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2314
Polymers36,7752
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)53.640, 53.640, 109.880
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: 18387.264 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
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: Jan 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→14.26 Å / Num. all: 9752 / Num. obs: 9674 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1420 / % possible all: 100

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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→14.26 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.594 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30913 968 10 %RANDOM
Rwork0.2385 ---
obs0.24529 8688 98.63 %-
all-9656 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.971 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→14.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 16 31 1297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021305
X-RAY DIFFRACTIONr_angle_refined_deg1.5222.0061768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.54826.78656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.00815254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.829153
X-RAY DIFFRACTIONr_chiral_restr0.10.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021935
LS refinement shellResolution: 2.201→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 71 -
Rwork0.335 540 -
obs--100 %

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