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- PDB-6xve: Engineered beta-lactoglobulin: variant F105L -

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Basic information

Entry
Database: PDB / ID: 6xve
TitleEngineered beta-lactoglobulin: variant F105L
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / 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 / 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsLoch, J.I. / Gotkowski, M. / 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 21, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionJan 29, 2020ID: 6RYS
Revision 1.0Jan 29, 2020Provider: 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


Theoretical massNumber of molelcules
Total (without water)18,1991
Polymers18,1991
Non-polymers00
Water95553
1
A: Beta-lactoglobulin

A: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,3982
Polymers36,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area880 Å2
ΔGint-9 kcal/mol
Surface area13520 Å2
Unit cell
Length a, b, c (Å)54.738, 79.771, 66.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

21A-251-

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 / Cell line (production host): Origami B (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P02754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 3.00 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: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→14.49 Å / Num. obs: 7984 / % possible obs: 98.6 % / Redundancy: 2.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.024 / Rrim(I) all: 0.039 / Net I/σ(I): 16.6 / Num. measured all: 16628 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.221.50.25310616900.8950.2380.349298.2
8.86-14.491.90.021165860.9980.0170.02774.466.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.15→14.49 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.602 / SU ML: 0.201 / SU R Cruickshank DPI: 0.3288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.259
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2915 993 12.4 %RANDOM
Rwork0.23 ---
obs0.2376 6990 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.32 Å2 / Biso mean: 35.878 Å2 / Biso min: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.15→14.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 53 1074
Biso mean---42.38 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131033
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171031
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.6411394
X-RAY DIFFRACTIONr_angle_other_deg1.2111.5812389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2845129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10124.47438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75315193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.315153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02178
LS refinement shellResolution: 2.15→2.205 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 59 -
Rwork0.295 528 -
all-587 -
obs--97.83 %
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)
11.607-0.58032.04520.7060.44146.0094-0.1766-0.26410.3985-0.08640.0352-0.275-0.2219-0.26860.14140.26370.0714-0.04490.1736-0.01820.186320.53299.90369.619
22.5793-0.0833-1.58030.5590.23281.8755-0.1664-0.0592-0.20090.0402-0.01790.04110.19230.12010.18430.09530.01340.02030.06680.01060.178715.7188.81375.799
33.19020.0597-2.3185.7897-6.369211.80330.11320.1941-0.2654-0.1037-0.18370.05520.2550.74820.07050.12430.0023-0.01740.1929-0.02830.114919.7887.33767.777
43.362.75061.351910.9712.25730.6960.10.42980.1841-0.3424-0.22890.5993-0.00880.09530.12890.2079-0.011-0.02770.2602-0.04220.066214.8289.47864.43
53.2413-0.2097-0.78651.3495-0.31262.2674-0.2365-0.02180.17920.17930.14020.0829-0.13110.15480.09630.12850.01460.01820.0539-0.02180.167115.28898.8678.686
61.72141.0568-0.65335.2321-1.99653.8557-0.078-0.21250.4298-0.02310.0601-0.0843-0.1407-0.88650.01790.03490.06860.01790.3046-0.0660.21433.81597.36778.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2A19 - 58
3X-RAY DIFFRACTION3A59 - 79
4X-RAY DIFFRACTION4A80 - 94
5X-RAY DIFFRACTION5A95 - 136
6X-RAY DIFFRACTION6A137 - 152

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