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- PDB-7z9z: Mutant L39Y of recombinant bovine beta-lactoglobulin in complex w... -

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Basic information

Entry
Database: PDB / ID: 7z9z
TitleMutant L39Y of recombinant bovine beta-lactoglobulin in complex with pramocaine
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / ligand / mutation / pramocaine
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 / Lipocalin signature.
Similarity search - Domain/homology
Pramocaine / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLoch, J.I. / Kurpiewska, K. / Bonarek, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Recognit. / Year: 2023
Title: beta-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies.
Authors: Bonarek, P. / Mularczyk, D. / Loch, J.I. / Kurpiewska, K. / Dziedzicka-Wasylewska, M.
History
DepositionMar 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7504
Polymers18,3251
Non-polymers4253
Water1,06359
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5008
Polymers36,6502
Non-polymers8506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1500 Å2
ΔGint-39 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.321, 53.321, 110.703
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11AAA-357-

HOH

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18325.111 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Plasmid: pET-Deut-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-PX9 / Pramocaine


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.4 M ammonium sulfate in 0.5 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54056 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.5→14.76 Å / Num. obs: 6648 / % possible obs: 98.9 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.124 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.61 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 796 / CC1/2: 0.723 / Rrim(I) all: 0.751

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.5→14.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.339 / SU ML: 0.256 / Cross valid method: FREE R-VALUE / ESU R: 0.85 / ESU R Free: 0.349
RfactorNum. reflection% reflection
Rfree0.2758 1013 15.302 %
Rwork0.2045 5607 -
all0.215 --
obs-6620 98.541 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.544 Å20.272 Å20 Å2
2--0.544 Å2-0 Å2
3----1.763 Å2
Refinement stepCycle: LAST / Resolution: 2.5→14.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 27 59 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131234
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161230
X-RAY DIFFRACTIONr_angle_refined_deg1.411.6481666
X-RAY DIFFRACTIONr_angle_other_deg1.131.5822855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1795148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84825.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.541153
X-RAY DIFFRACTIONr_chiral_restr0.0550.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
X-RAY DIFFRACTIONr_nbd_refined0.180.2209
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21109
X-RAY DIFFRACTIONr_nbtor_refined0.1560.2552
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.28
X-RAY DIFFRACTIONr_nbd_other0.2620.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.25
X-RAY DIFFRACTIONr_mcbond_it2.6483.795595
X-RAY DIFFRACTIONr_mcbond_other2.6383.793594
X-RAY DIFFRACTIONr_mcangle_it4.2135.668739
X-RAY DIFFRACTIONr_mcangle_other4.2115.67740
X-RAY DIFFRACTIONr_scbond_it3.2734.304639
X-RAY DIFFRACTIONr_scbond_other3.2144.275636
X-RAY DIFFRACTIONr_scangle_it5.4036.261926
X-RAY DIFFRACTIONr_scangle_other5.3566.214921
X-RAY DIFFRACTIONr_lrange_it8.1243.681284
X-RAY DIFFRACTIONr_lrange_other8.09843.6391279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5630.421030.3443760.3614790.6630.6921000.348
2.563-2.6310.391620.3193830.3294450.7160.7621000.324
2.631-2.7050.285720.313790.3064510.8430.8041000.301
2.705-2.7850.396620.2643700.2844320.7910.8461000.256
2.785-2.8730.394680.2743460.2934140.7980.8581000.265
2.873-2.970.351660.2393520.2564180.840.8941000.229
2.97-3.0770.295600.2263560.2364160.8750.9011000.213
3.077-3.1970.285350.2183340.2243690.8930.9121000.207
3.197-3.3320.309720.2153090.2313810.8790.9261000.21
3.332-3.4860.318460.1842910.23370.8780.9471000.177
3.486-3.6630.208640.182780.1853420.9440.9591000.175
3.663-3.8710.295320.192980.1993300.9160.9511000.183
3.871-4.1180.242360.1752740.1833100.9290.9451000.17
4.118-4.4190.191450.1632480.1672930.9590.9611000.157
4.419-4.7980.202480.1292230.1412730.9550.97799.26740.124
4.798-5.2950.209340.1662140.1722510.9460.96198.80480.159
5.295-5.9870.404340.2211900.2432290.8660.94997.81660.211
5.987-7.0480.288270.2211620.2311990.9340.94894.97490.204
7.048-8.9950.2350.1681270.1751740.9590.96793.10340.16
8.995-14.760.168120.191970.1881260.9670.96586.50790.188

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