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

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Basic information

Entry
Database: PDB / ID: 7zlf
TitleMutant L39Y-L58F of recombinant bovine beta-lactoglobulin in complex with endogenous fatty acid
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / mutation / ligand
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
LAURIC ACID / 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
DepositionApr 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 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)18,7736
Polymers18,3171
Non-polymers4565
Water1,09961
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 37.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)37,54612
Polymers36,6342
Non-polymers91210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)53.245, 53.245, 111.210
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-332-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#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 (cattle) / Gene: LGB / Plasmid: pET-DUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.4 M 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 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.1→15.21 Å / Num. obs: 11150 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.122 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 898 / CC1/2: 0.631 / Rrim(I) all: 1.181 / % possible all: 99.7

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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→15.21 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.72 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.186
RfactorNum. reflection% reflection
Rfree0.2374 1052 9.454 %
Rwork0.1912 10076 -
all0.196 --
obs-11128 99.357 %
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: 38.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.397 Å20.198 Å2-0 Å2
2--0.397 Å20 Å2
3----1.287 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 28 61 1305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131261
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161245
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.6491696
X-RAY DIFFRACTIONr_angle_other_deg1.2481.5832889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70825.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72515236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.936153
X-RAY DIFFRACTIONr_chiral_restr0.0720.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_nbd_refined0.20.2207
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21097
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2564
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.24
X-RAY DIFFRACTIONr_nbd_other0.2310.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.27
X-RAY DIFFRACTIONr_mcbond_it2.0133.101609
X-RAY DIFFRACTIONr_mcbond_other2.0033.099608
X-RAY DIFFRACTIONr_mcangle_it3.174.627756
X-RAY DIFFRACTIONr_mcangle_other3.1694.629757
X-RAY DIFFRACTIONr_scbond_it2.4773.524652
X-RAY DIFFRACTIONr_scbond_other2.4543.494649
X-RAY DIFFRACTIONr_scangle_it4.0415.122940
X-RAY DIFFRACTIONr_scangle_other4.0235.072935
X-RAY DIFFRACTIONr_lrange_it6.14735.6171275
X-RAY DIFFRACTIONr_lrange_other6.12535.5441271
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
2.1-2.1540.34620.2777280.2827940.7580.79499.49620.268
2.154-2.2110.296770.2687020.2717840.810.82799.36220.259
2.211-2.2740.296650.246780.2457470.8430.87399.46450.228
2.274-2.3430.289570.2476650.257250.8790.88399.58620.231
2.343-2.4170.325640.2426660.2497340.8470.89299.4550.228
2.417-2.50.323530.2366220.2426760.8760.90499.85210.213
2.5-2.5920.288680.1975950.2066630.9090.9331000.188
2.592-2.6940.297590.2125860.226460.9190.93299.84520.193
2.694-2.810.296750.2155590.2256340.9080.9241000.2
2.81-2.9420.223560.1975540.1996100.9170.9381000.191
2.942-3.0950.233590.195050.1955640.9390.9451000.183
3.095-3.2740.229450.1734920.1785370.9420.9581000.168
3.274-3.4890.156700.1794390.1765090.9580.9581000.178
3.489-3.7520.26410.1794460.1864870.9280.9591000.179
3.752-4.0850.196440.1584130.1624570.9560.9621000.16
4.085-4.5270.182460.1413670.1464140.9640.97499.75850.144
4.527-5.1520.18320.1463460.1493780.9660.9771000.153
5.152-6.1360.296320.1932940.2023260.9340.961000.201
6.136-8.0470.241280.1982440.2032720.9240.9551000.206
8.047-15.210.263190.1971740.2041980.960.96697.47470.214
Refinement TLS params.Method: refined / Origin x: -15.2183 Å / Origin y: 4.9196 Å / Origin z: 3.5662 Å
111213212223313233
T0.0946 Å2-0.0481 Å2-0.0299 Å2-0.0347 Å20.0194 Å2--0.0199 Å2
L0.1855 °20.0912 °20.4031 °2-1.085 °20.3023 °2--1.3017 °2
S-0.0891 Å °0.0734 Å °0.0495 Å °-0.0268 Å °-0.0011 Å °0.0997 Å °-0.0366 Å °0.1186 Å °0.0903 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 162
2X-RAY DIFFRACTION1ALLAAA201
3X-RAY DIFFRACTION1ALLAAA202

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