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- PDB-6qi6: Trigonal form of WT recombinant bovine beta-lactoglobulin -

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Basic information

Entry
Database: PDB / ID: 6qi6
TitleTrigonal form of WT recombinant bovine beta-lactoglobulin
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / lipocalin / recombinant protein
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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ETHANOL / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLoch, J.I. / Krawczyk, A. / Lewinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2012/05/B/ST5/00278 Poland
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structure-based design approach to rational site-directed mutagenesis of beta-lactoglobulin.
Authors: Bonarek, P. / Loch, J.I. / Tworzydlo, M. / Cooper, D.R. / Milto, K. / Wrobel, P. / Kurpiewska, K. / Lewinski, K.
History
DepositionJan 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 29, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4034
Polymers18,2331
Non-polymers1703
Water1,36976
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8068
Polymers36,4662
Non-polymers3406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)52.732, 52.732, 110.330
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: 18233.016 Da / Num. of mol.: 1 / Mutation: L1A, I2S
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 / References: UniProt: P02754
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.80 M (NH4)2SO4 in 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→14.07 Å / Num. obs: 12441 / % possible obs: 99.2 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.034 / Rrim(I) all: 0.06 / Net I/σ(I): 9.5 / Num. measured all: 31832 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.051.90.4059290.6810.3770.55597.8
8.72-14.072.10.0241270.9930.020.03270.1

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HTD

5htd


Resolution: 2→14.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.356 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1791 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.174
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1218 9.8 %RANDOM
Rwork0.1857 ---
obs0.1917 11200 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.28 Å2 / Biso mean: 38.813 Å2 / Biso min: 19.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2→14.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 11 76 1295
Biso mean--62.01 43.61 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131237
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171204
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.6451670
X-RAY DIFFRACTIONr_angle_other_deg1.2881.5782803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1635153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32325.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23615232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.801153
X-RAY DIFFRACTIONr_chiral_restr0.0780.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02213
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 106 -
Rwork0.249 741 -
all-847 -
obs--96.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.97872.1023-0.49134.16642.92913.0561-0.04310.2308-0.2554-0.1193-0.13210.0501-0.083-0.25920.17530.1275-0.0507-0.08510.11070.01080.0793-24.5392.943-4.198
20.5898-0.74260.22682.49490.34332.6356-0.19190.10160.14370.08190.0751-0.35980.02270.36780.11670.116-0.0665-0.03090.10530.02960.0687-8.1516.6353.632
312.80743.5651.04756.6893-0.40151.8451-0.18930.7436-0.1474-0.47140.2413-0.2030.14310.2559-0.05210.1932-0.038-0.00290.17150.00660.0298-16.264-0.272-9.735
480.418-26.84250.80119.4702-0.52330.14720.80932.35680.46-0.8766-1.087-0.75390.33570.16560.27770.89420.34620.57510.52870.18830.986-6.722-5.901-5.757
50.7969-0.16860.75343.04870.63782.6936-0.08260.1170.0110.1889-0.02330.27040.0585-0.01190.10580.0844-0.0525-0.00670.04460.01250.0332-18.4475.6667.967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 15
2X-RAY DIFFRACTION2A16 - 70
3X-RAY DIFFRACTION3A71 - 82
4X-RAY DIFFRACTION4A83 - 88
5X-RAY DIFFRACTION5A89 - 162

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