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- PDB-4y0r: Bovine beta-lactoglobulin complex with pramocaine crystallized fr... -

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Basic information

Entry
Database: PDB / ID: 4y0r
TitleBovine beta-lactoglobulin complex with pramocaine crystallized from ammonium sulphate (BLG-PRM2)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT / LIGAND BINDING
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
Pramocaine / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLoch, J.I. / Bonarek, P. / Polit, A. / Jablonski, M. / Czub, M. / Ye, X. / Lewinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre (NCN) Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2015
Title: beta-Lactoglobulin interactions with local anaesthetic drugs - Crystallographic and calorimetric studies.
Authors: Loch, J.I. / Bonarek, P. / Polit, A. / Jabonski, M. / Czub, M. / Ye, X. / Lewinski, K.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5952
Polymers18,3011
Non-polymers2931
Water95553
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1894
Polymers36,6022
Non-polymers5872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)53.735, 53.735, 110.738
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

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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-PX9 / Pramocaine


Mass: 293.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: protein 20 mg/ml, 2.4 M (NH4)2SO4 in 0.5 M Tris-HCl pH 8.9 and 5 mM pramociane

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→13.43 Å / Num. obs: 8567 / % possible obs: 98.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 2.6 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
CrysalisProdata collection
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.3→13.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.054 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28549 1050 12.3 %RANDOM
Rwork0.21223 ---
obs0.22128 7517 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→13.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 21 53 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021268
X-RAY DIFFRACTIONr_bond_other_d0.0010.021261
X-RAY DIFFRACTIONr_angle_refined_deg1.4952.0091710
X-RAY DIFFRACTIONr_angle_other_deg0.78832925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92526.53852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.37515242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.557153
X-RAY DIFFRACTIONr_chiral_restr0.0730.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4273.716617
X-RAY DIFFRACTIONr_mcbond_other2.4293.716616
X-RAY DIFFRACTIONr_mcangle_it3.9545.544766
X-RAY DIFFRACTIONr_mcangle_other3.9525.545767
X-RAY DIFFRACTIONr_scbond_it2.1233.96651
X-RAY DIFFRACTIONr_scbond_other2.1213.964652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6035.831945
X-RAY DIFFRACTIONr_long_range_B_refined5.94729.1921354
X-RAY DIFFRACTIONr_long_range_B_other5.94529.2211355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 67 -
Rwork0.242 534 -
obs--97.72 %

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