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- PDB-7za0: Mutant L58F of recombinant bovine beta-lactoglobulin in complex w... -

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Basic information

Entry
Database: PDB / ID: 7za0
TitleMutant L58F 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 space / 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 (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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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)18,6563
Polymers18,2671
Non-polymers3892
Water2,342130
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 37.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)37,3136
Polymers36,5342
Non-polymers7794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)53.722, 53.722, 112.254
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / / Beta-LG


Mass: 18267.031 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L58F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-PX9 / Pramocaine / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.2 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: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.1→13.84 Å / Num. obs: 11346 / % possible obs: 99 % / Redundancy: 2.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.052 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 933 / CC1/2: 0.78 / Rrim(I) all: 0.491 / % possible all: 98.6

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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: 2.1→13.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.388 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.179
RfactorNum. reflection% reflection
Rfree0.2242 1058 9.342 %
Rwork0.1747 10267 -
all0.179 --
obs-11325 98.401 %
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: 39.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.585 Å2
Refinement stepCycle: LAST / Resolution: 2.1→13.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 26 130 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131262
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161244
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6481702
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5832887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03625.53656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51115238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.611153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_nbd_refined0.1940.2202
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21120
X-RAY DIFFRACTIONr_nbtor_refined0.1590.2571
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.277
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0480.22
X-RAY DIFFRACTIONr_nbd_other0.2290.218
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.210
X-RAY DIFFRACTIONr_mcbond_it2.3072.918609
X-RAY DIFFRACTIONr_mcbond_other2.3072.917608
X-RAY DIFFRACTIONr_mcangle_it3.6164.348756
X-RAY DIFFRACTIONr_mcangle_other3.6144.349757
X-RAY DIFFRACTIONr_scbond_it2.93.434653
X-RAY DIFFRACTIONr_scbond_other2.8983.415650
X-RAY DIFFRACTIONr_scangle_it4.8314.954946
X-RAY DIFFRACTIONr_scangle_other4.8384.919941
X-RAY DIFFRACTIONr_lrange_it6.73634.6471303
X-RAY DIFFRACTIONr_lrange_other6.61334.2981284
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
2.1-2.1540.292700.2667490.2688360.8120.80797.96650.269
2.154-2.2110.334900.2526870.267870.8180.86198.72940.251
2.211-2.2740.24510.2216980.2237540.8970.89699.33690.218
2.274-2.3420.26570.2167050.227730.8890.90598.5770.211
2.342-2.4160.261540.2096570.2137160.8860.91699.30170.201
2.416-2.4980.25660.1976350.2027060.9250.9399.29180.184
2.498-2.5890.328650.2026320.2136990.850.91199.71390.187
2.589-2.6910.291610.2055930.2146590.9020.91699.24130.191
2.691-2.8060.257780.1925510.26290.9230.9351000.178
2.806-2.9370.206460.1475700.1526160.960.9641000.134
2.937-3.0880.219420.175390.1735810.9410.9541000.158
3.088-3.2650.259500.174980.1785480.9270.9451000.163
3.265-3.4770.194620.1624790.1665430.9550.96299.63170.155
3.477-3.7360.196720.164220.1654970.960.96799.39640.155
3.736-4.0630.183430.1494160.1524640.9590.96998.92240.145
4.063-4.4940.159460.1323750.1344270.9680.9898.59480.126
4.494-5.10.179310.1263380.133800.9680.98297.10530.123
5.1-6.0450.224210.2113150.2123460.9390.95197.10980.208
6.045-7.8340.37280.1732430.1892860.8970.96294.75520.169
7.834-13.840.164250.1661650.1662070.9690.97591.78740.162
Refinement TLS params.Method: refined / Origin x: -15.5929 Å / Origin y: 4.6352 Å / Origin z: 3.5473 Å
111213212223313233
T0.1676 Å2-0.0416 Å2-0.0183 Å2-0.0488 Å20.0226 Å2--0.0139 Å2
L0.2099 °20.3531 °20.1793 °2-0.9988 °20.3613 °2--1.3613 °2
S-0.1518 Å °0.0428 Å °0.0352 Å °-0.1061 Å °0.0566 Å °0.0819 Å °-0.047 Å °0.1638 Å °0.0952 Å °
Refinement TLS groupSelection: ALL

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