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- PDB-7bgz: Mutant L39K of recombinant beta-lactoglobulin in complex with end... -

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Basic information

Entry
Database: PDB / ID: 7bgz
TitleMutant L39K 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
DECANOIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.401 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)18,4833
Polymers18,2491
Non-polymers2342
Water88349
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9676
Polymers36,4982
Non-polymers4694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)53.560, 53.560, 110.880
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: 18249.037 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39K
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): Origami B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3.0 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: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→14.26 Å / Num. obs: 7446 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Net I/σ(I): 12.9 / Num. measured all: 26085 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.492.50.6531.418667540.7140.5020.831.497.6
8.98-14.262.20.01527112310.0120.0235.771

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.4 Å14.26 Å
Translation2.4 Å14.26 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: 2.401→13.753 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.452 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.297
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1075 14.455 %RANDOM
Rwork0.1938 6362 --
all0.204 ---
obs0.20297 7437 97.279 %-
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: 50.562 Å2
Baniso -1Baniso -2Baniso -3
1--0.213 Å2-0.106 Å2-0 Å2
2---0.213 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.401→13.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 16 49 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131183
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171157
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6441598
X-RAY DIFFRACTIONr_angle_other_deg1.2331.582671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.945146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.422548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30115208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.348153
X-RAY DIFFRACTIONr_chiral_restr0.0750.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02226
X-RAY DIFFRACTIONr_nbd_refined0.1980.2203
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21014
X-RAY DIFFRACTIONr_nbtor_refined0.1590.2514
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2576
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.243
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.28
X-RAY DIFFRACTIONr_nbd_other0.2430.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.23
X-RAY DIFFRACTIONr_mcbond_it2.463.533596
X-RAY DIFFRACTIONr_mcbond_other2.463.532595
X-RAY DIFFRACTIONr_mcangle_it3.9725.264738
X-RAY DIFFRACTIONr_mcangle_other3.975.265739
X-RAY DIFFRACTIONr_scbond_it2.4563.782587
X-RAY DIFFRACTIONr_scbond_other2.4543.785588
X-RAY DIFFRACTIONr_scangle_it45.545860
X-RAY DIFFRACTIONr_scangle_other3.9975.547861
X-RAY DIFFRACTIONr_lrange_it5.95440.1891175
X-RAY DIFFRACTIONr_lrange_other5.9540.1271174
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
2.401-2.4610.366970.3284280.3355420.7810.7896.86350.315
2.461-2.5270.348580.2874370.2945130.6940.80496.49120.274
2.527-2.5970.485510.2754300.2954960.7890.86496.97580.252
2.597-2.6740.361660.2794380.295190.8250.86497.10980.254
2.674-2.7580.343780.243690.2584590.8440.88397.38560.213
2.758-2.8510.337670.2253940.2414730.860.89597.4630.201
2.851-2.9540.279760.2043680.2164530.9010.92698.01320.177
2.954-3.0690.318640.2223580.2374300.8670.90398.13950.2
3.069-3.1980.285540.213560.2214180.90.91698.08610.188
3.198-3.3450.28480.2183650.2254200.8920.91798.33330.201
3.345-3.5140.291480.2053190.2163730.9030.93198.39140.193
3.514-3.7120.236620.1923180.23850.9470.94898.70130.181
3.712-3.9480.26430.192950.1993420.9250.94698.83040.178
3.948-4.2360.198660.1522670.1623360.9520.9799.10710.142
4.236-4.5960.151420.1142590.123020.9790.9899.66890.111
4.596-5.0690.209280.132600.1372890.9620.97899.6540.132
5.069-5.7250.377300.2132260.2312580.8770.93899.22480.205
5.725-6.7260.419330.2142010.2382370.8610.93898.73420.209
6.726-8.5450.214360.1531530.1651910.9590.96698.95290.159
8.545-13.7530.227260.1841170.1931500.9530.96595.33330.202
Refinement TLS params.Method: refined / Origin x: 15.4893 Å / Origin y: 5.1748 Å / Origin z: 33.3413 Å
111213212223313233
T0.3313 Å20.1697 Å2-0.0061 Å2-0.1354 Å2-0.0316 Å2--0.0201 Å2
L0.8761 °20.4496 °20.77 °2-1.5374 °2-0.4822 °2--2.6925 °2
S-0.3844 Å °-0.1764 Å °-0.0333 Å °0.1513 Å °0.2618 Å °-0.149 Å °-0.2347 Å °-0.407 Å °0.1226 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 162
2X-RAY DIFFRACTION1ALLAaA201

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