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- PDB-4y0s: Goat beta-lactoglobulin complex with pramocaine (GLG-PRM) -

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Basic information

Entry
Database: PDB / ID: 4y0s
TitleGoat beta-lactoglobulin complex with pramocaine (GLG-PRM)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


retinol 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 speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 23, 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)18,6984
Polymers18,2121
Non-polymers4863
Water1,856103
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3958
Polymers36,4242
Non-polymers9716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)53.113, 53.113, 111.148
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-318-

HOH

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18212.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: P02756
#2: Chemical ChemComp-PX9 / Pramocaine


Mass: 293.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27NO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: protein 10 mg/ml, 2.30 M (NH4)2SO4 in 0.5 Tris-HCl pH 8.5, 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: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→13.07 Å / Num. obs: 14765 / % possible obs: 99.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.3 / % possible all: 99

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Processing

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

1bsy


Resolution: 1.9→13.07 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.303 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26532 1481 10 %RANDOM
Rwork0.21332 ---
obs0.21854 13284 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.131 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→13.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 31 103 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021302
X-RAY DIFFRACTIONr_bond_other_d0.0010.021307
X-RAY DIFFRACTIONr_angle_refined_deg1.3382.0151762
X-RAY DIFFRACTIONr_angle_other_deg0.73833029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14126.53852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44815249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.044153
X-RAY DIFFRACTIONr_chiral_restr0.080.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
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_it1.7522.413630
X-RAY DIFFRACTIONr_mcbond_other1.7512.411629
X-RAY DIFFRACTIONr_mcangle_it2.8753.601785
X-RAY DIFFRACTIONr_mcangle_other2.8753.602786
X-RAY DIFFRACTIONr_scbond_it1.8132.706671
X-RAY DIFFRACTIONr_scbond_other1.8172.698664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0083.945964
X-RAY DIFFRACTIONr_long_range_B_refined5.05619.6791466
X-RAY DIFFRACTIONr_long_range_B_other4.87519.5191438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 108 -
Rwork0.33 924 -
obs--98.1 %

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