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- PDB-7bgx: Mutant F105L of recombinant beta-lactoglobulin -

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Basic information

Entry
Database: PDB / ID: 7bgx
TitleMutant F105L of recombinant beta-lactoglobulin
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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLoch, J.I. / Wrobel, P. / 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 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / diffrn_source
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 / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
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)18,4794
Polymers18,1991
Non-polymers2803
Water1,06359
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9588
Polymers36,3982
Non-polymers5616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2500 Å2
ΔGint-31 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.790, 52.790, 108.820
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-458-

HOH

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Components

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


Mass: 18198.998 Da / Num. of mol.: 1 / Mutation: L1A, I2S, F105L
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(DE3) (bacteria) / Variant (production host): Origami B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 59 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.4 M ammonium sulfate in 0.5 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2→19.65 Å / Num. obs: 12244 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Net I/σ(I): 11 / Num. measured all: 40044 / Scaling rejects: 33
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
2-2.052.60.6371.723509100.4650.4720.7971.799.3
8.95-19.6540.0275861460.9990.0140.0334.587.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.91 Å19.65 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2→19.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.496 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1088 8.91 %RANDOM
Rwork0.2002 11123 --
all0.204 ---
obs0.20432 12211 98.23 %-
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: 39.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.011 Å2-0.006 Å2-0 Å2
2---0.011 Å20 Å2
3---0.036 Å2
Refinement stepCycle: LAST / Resolution: 2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 17 59 1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131208
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171170
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.6371642
X-RAY DIFFRACTIONr_angle_other_deg1.3791.5762694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9625153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01725.10647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69815208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.243153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
X-RAY DIFFRACTIONr_nbd_refined0.1970.2260
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21125
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2562
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.27
X-RAY DIFFRACTIONr_nbd_other0.2840.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.22
X-RAY DIFFRACTIONr_mcbond_it2.3953.147618
X-RAY DIFFRACTIONr_mcbond_other2.3963.146617
X-RAY DIFFRACTIONr_mcangle_it3.7734.696769
X-RAY DIFFRACTIONr_mcangle_other3.7724.698770
X-RAY DIFFRACTIONr_scbond_it2.5563.418590
X-RAY DIFFRACTIONr_scbond_other2.5083.385587
X-RAY DIFFRACTIONr_scangle_it4.0925.007873
X-RAY DIFFRACTIONr_scangle_other4.0144.951868
X-RAY DIFFRACTIONr_lrange_it6.70938.1011305
X-RAY DIFFRACTIONr_lrange_other6.68637.9951298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.304750.289818X-RAY DIFFRACTION98.8926
2.052-2.1070.281710.28790X-RAY DIFFRACTION98.7385
2.107-2.1680.34770.29734X-RAY DIFFRACTION99.6315
2.168-2.2340.236700.236763X-RAY DIFFRACTION99.6412
2.234-2.3060.335650.243748X-RAY DIFFRACTION99.8772
2.306-2.3860.265700.248681X-RAY DIFFRACTION100
2.386-2.4740.312790.248681X-RAY DIFFRACTION100
2.474-2.5740.27550.237669X-RAY DIFFRACTION100
2.574-2.6860.307760.22614X-RAY DIFFRACTION99.5671
2.686-2.8140.286540.217613X-RAY DIFFRACTION100
2.814-2.9630.265630.198568X-RAY DIFFRACTION98.5938
2.963-3.1390.274610.2532X-RAY DIFFRACTION98.1788
3.139-3.3490.184400.18517X-RAY DIFFRACTION98.2363
3.349-3.6090.179450.179472X-RAY DIFFRACTION96.6355
3.609-3.940.219420.174431X-RAY DIFFRACTION94.7896
3.94-4.3830.188390.145405X-RAY DIFFRACTION94.6695
4.383-5.020.183290.123350X-RAY DIFFRACTION94.2786
5.02-6.050.274390.208305X-RAY DIFFRACTION93.2249
6.05-8.1770.276250.221248X-RAY DIFFRACTION95.4545
8.177-19.650.24130.181182X-RAY DIFFRACTION95.1219
Refinement TLS params.Method: refined / Origin x: -11.5547 Å / Origin y: -10.389 Å / Origin z: -14.7686 Å
111213212223313233
T0.1465 Å20.0883 Å2-0.0332 Å2-0.0856 Å2-0.0133 Å2--0.0124 Å2
L1.0781 °2-0.5464 °2-0.4731 °2-0.5168 °20.6542 °2--1.5751 °2
S-0.034 Å °-0.0613 Å °-0.0619 Å °-0.1507 Å °-0.0466 Å °0.0744 Å °-0.1423 Å °0.0982 Å °0.0806 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 162
2X-RAY DIFFRACTION1ALLAaA301

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