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- PDB-7bh0: Mutant L39Y of recombinant beta-lactoglobulin in complex with end... -

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Basic information

Entry
Database: PDB / ID: 7bh0
TitleMutant L39Y of recombinant beta-lactoglobulin in complex with endogenous ligand
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / beta-lactoglobulin / lipocalin / mutation
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 / molecular replacement / Resolution: 2.1 Å
AuthorsLoch, J.I. / Siuda, M.K. / Lewinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2012/05/B/ST5/00278 Poland
CitationJournal: Acta Biochim.Pol. / Year: 2021
Title: Interactions of new lactoglobulin variants with tetracaine: crystallographic studies of ligand binding to lactoglobulin mutants possessing single substitution in the binding pocket.
Authors: Loch, J. / Bonarek, P. / Siuda, M. / Wrobel, P. / Lewinski, K.
History
DepositionJan 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,5193
Polymers18,2831
Non-polymers2362
Water1,54986
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0386
Polymers36,5662
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)53.270, 53.270, 109.890
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-356-

HOH

21AAA-364-

HOH

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18283.031 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Origamiam B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 2.2 M ammonium sulfate in 0.5 M Tris-HCl pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→13.74 Å / Num. obs: 11001 / % possible obs: 99.4 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Net I/σ(I): 7.7 / Num. measured all: 29177 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.162.10.22328960.8840.1990.398.5
8.66-13.742.20.0331400.9960.0250.04172.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å13.66 Å
Translation2 Å13.66 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.1→13.661 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.511 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.214
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 1066 9.708 %RANDOM
Rwork0.2008 9915 --
all0.208 ---
obs0.208 10981 99.133 %-
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: 36.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.075 Å20.037 Å20 Å2
2--0.075 Å2-0 Å2
3----0.243 Å2
Refinement stepCycle: LAST / Resolution: 2.1→13.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 15 86 1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131195
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171133
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6411623
X-RAY DIFFRACTIONr_angle_other_deg1.2391.572613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2195149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04925.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54715198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.997153
X-RAY DIFFRACTIONr_chiral_restr0.070.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021327
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02235
X-RAY DIFFRACTIONr_nbd_refined0.210.2208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21017
X-RAY DIFFRACTIONr_nbtor_refined0.1570.2548
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.210
X-RAY DIFFRACTIONr_nbd_other0.2940.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.27
X-RAY DIFFRACTIONr_mcbond_it7.6072.297605
X-RAY DIFFRACTIONr_mcbond_other7.6032.296604
X-RAY DIFFRACTIONr_mcangle_it8.6313.394751
X-RAY DIFFRACTIONr_mcangle_other8.6253.395752
X-RAY DIFFRACTIONr_scbond_it10.2482.857590
X-RAY DIFFRACTIONr_scbond_other10.242.857591
X-RAY DIFFRACTIONr_scangle_it11.4334.014872
X-RAY DIFFRACTIONr_scangle_other11.4274.015873
X-RAY DIFFRACTIONr_lrange_it11.80728.0851223
X-RAY DIFFRACTIONr_lrange_other11.82127.831214
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
2.1-2.1530.285710.2416920.2457820.8780.87797.57030.239
2.153-2.2110.337820.2476900.2567790.8360.85799.10140.239
2.211-2.2730.309550.2426490.2487060.8470.87699.71670.239
2.273-2.3410.341800.2436480.2537330.8490.88699.31790.234
2.341-2.4150.333670.2376470.2467140.8690.8981000.23
2.415-2.4970.357700.2396110.2526820.8370.8799.85340.232
2.497-2.5880.319540.2385950.2456490.8390.871000.227
2.588-2.690.368700.2415710.2556420.810.86999.84420.233
2.69-2.8050.325490.2485750.2546240.7960.8641000.24
2.805-2.9350.309660.2165160.2265820.8840.9151000.216
2.935-3.0860.318560.225020.235580.8660.9071000.218
3.086-3.2630.289490.2234960.2295450.8910.9171000.223
3.263-3.4740.262510.2014560.2075070.920.9381000.204
3.474-3.7330.244460.1894310.1944770.920.9481000.196
3.733-4.0590.195480.1674050.174530.9630.9591000.175
4.059-4.4880.218370.1393730.1464100.9510.9671000.147
4.488-5.0920.227290.1393400.1453690.9570.9731000.152
5.092-6.030.304270.22980.2073250.9220.9611000.201
6.03-7.8020.255250.1892550.1952800.9470.9611000.196
7.802-13.6610.208340.1531610.1622030.9590.97396.05910.17
Refinement TLS params.Method: refined / Origin x: 15.2489 Å / Origin y: 4.9936 Å / Origin z: 32.9951 Å
111213212223313233
T0.2352 Å20.1014 Å2-0.0414 Å2-0.0884 Å2-0.0315 Å2--0.0423 Å2
L0.3936 °2-0.089 °20.757 °2-1.1622 °2-0.451 °2--1.6331 °2
S-0.1575 Å °-0.1724 Å °0.0288 Å °0.0398 Å °0.093 Å °-0.2075 Å °-0.1299 Å °-0.3189 Å °0.0646 Å °
Refinement TLS groupSelection: ALL

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