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- PDB-7zcd: Mutant L39Y-L58F of recombinant bovine beta-lactoglobulin in comp... -

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Basic information

Entry
Database: PDB / ID: 7zcd
TitleMutant L39Y-L58F of recombinant bovine beta-lactoglobulin in complex with pramocaine
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / mutation / ligand
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: 2.1 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 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 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 1.4Nov 13, 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)18,7073
Polymers18,3171
Non-polymers3892
Water1,00956
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4136
Polymers36,6342
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)53.551, 53.551, 110.866
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-354-

HOH

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18317.047 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y, L58F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic 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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.2M ammonium sulfate, 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: 2.1→14.99 Å / Num. obs: 11262 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 1.373 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 919 / CC1/2: 0.654 / Rrim(I) all: 1.551

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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→14.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.246 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.248 / ESU R Free: 0.209
RfactorNum. reflection% reflection
Rfree0.2689 1057 9.411 %
Rwork0.2231 10174 -
all0.227 --
obs-11231 99.442 %
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: 45.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.264 Å20.132 Å20 Å2
2--0.264 Å2-0 Å2
3----0.855 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 26 56 1299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131265
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161241
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.651706
X-RAY DIFFRACTIONr_angle_other_deg1.1661.5822880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3615150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8525.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22115237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.334153
X-RAY DIFFRACTIONr_chiral_restr0.0620.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02249
X-RAY DIFFRACTIONr_nbd_refined0.1910.2208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21121
X-RAY DIFFRACTIONr_nbtor_refined0.160.2567
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.261
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.26
X-RAY DIFFRACTIONr_nbd_other0.220.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.25
X-RAY DIFFRACTIONr_mcbond_it1.7473.214609
X-RAY DIFFRACTIONr_mcbond_other1.7483.214608
X-RAY DIFFRACTIONr_mcangle_it2.9354.797756
X-RAY DIFFRACTIONr_mcangle_other2.9344.798757
X-RAY DIFFRACTIONr_scbond_it1.813.556656
X-RAY DIFFRACTIONr_scbond_other1.7933.523653
X-RAY DIFFRACTIONr_scangle_it3.0985.214950
X-RAY DIFFRACTIONr_scangle_other3.0755.159945
X-RAY DIFFRACTIONr_lrange_it5.61736.7621313
X-RAY DIFFRACTIONr_lrange_other5.60736.7041308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1530.421630.355738X-RAY DIFFRACTION99.2565
2.153-2.2110.368750.333708X-RAY DIFFRACTION99.7452
2.211-2.2740.35700.313685X-RAY DIFFRACTION99.7358
2.274-2.3420.382520.308686X-RAY DIFFRACTION100
2.342-2.4170.393690.294660X-RAY DIFFRACTION100
2.417-2.50.301450.286638X-RAY DIFFRACTION100
2.5-2.5910.376720.257603X-RAY DIFFRACTION100
2.591-2.6940.333630.27594X-RAY DIFFRACTION99.848
2.694-2.8090.33670.27568X-RAY DIFFRACTION99.8428
2.809-2.9410.339630.235517X-RAY DIFFRACTION100
2.941-3.0940.303580.246539X-RAY DIFFRACTION100
3.094-3.2730.272470.232481X-RAY DIFFRACTION100
3.273-3.4870.238700.223452X-RAY DIFFRACTION100
3.487-3.7490.267430.196454X-RAY DIFFRACTION100
3.749-4.0820.187440.177412X-RAY DIFFRACTION100
4.082-4.5220.213420.159372X-RAY DIFFRACTION100
4.522-5.1440.161350.158347X-RAY DIFFRACTION100
5.144-6.1220.315330.209297X-RAY DIFFRACTION100
6.122-8.0150.242280.21248X-RAY DIFFRACTION100
8.015-14.990.236180.183175X-RAY DIFFRACTION96.0199
Refinement TLS params.Method: refined / Origin x: -15.5529 Å / Origin y: 4.5825 Å / Origin z: 3.5356 Å
111213212223313233
T0.2755 Å2-0.0724 Å2-0.0448 Å2-0.0876 Å20.0396 Å2--0.0448 Å2
L0.2681 °2-0.03 °20.436 °2-1.1389 °20.3909 °2--1.9235 °2
S-0.216 Å °0.0827 Å °0.0109 Å °-0.1562 Å °0.1007 Å °0.2108 Å °-0.1482 Å °0.3082 Å °0.1152 Å °
Refinement TLS groupSelection: ALL

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