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- PDB-6ryt: Engineered beta-lactoglobulin: variant M107L -

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Basic information

Entry
Database: PDB / ID: 6ryt
TitleEngineered beta-lactoglobulin: variant M107L
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / Lipocalin / mutation / lactoglobulin
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
PHOSPHATE ION / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLoch, J.I. / Kurpiewska, K. / 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
DepositionJun 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Data collection / Database references / Category: citation / citation_author / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7095
Polymers36,4302
Non-polymers2793
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.160, 61.520, 78.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-201-

PO4

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18214.977 Da / Num. of mol.: 2 / Mutation: L1A, I2S, M107L
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 / References: UniProt: P02754
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.60 M (NH4)2SO4 in 0.1 Tris-HCl pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976225 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976225 Å / Relative weight: 1
ReflectionResolution: 2.1→78.24 Å / Num. obs: 15140 / % possible obs: 93.1 % / Redundancy: 3.2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.06 / Rrim(I) all: 0.118 / Net I/σ(I): 4.7 / Num. measured all: 49058 / Scaling rejects: 133
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
2.1-2.163.20.471406412510.8460.2990.563295.6
8.91-78.2430.0536552210.9750.0360.0658.284.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.1→48.41 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 17.853 / SU ML: 0.217 / SU R Cruickshank DPI: 0.3365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.254
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 1366 9 %RANDOM
Rwork0.2144 ---
obs0.2204 13740 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.44 Å2 / Biso mean: 39.768 Å2 / Biso min: 15.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.1→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 17 40 2299
Biso mean--67.83 38.58 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172258
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.643084
X-RAY DIFFRACTIONr_angle_other_deg1.1771.5815258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0155281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12825.16591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39615432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.326156
X-RAY DIFFRACTIONr_chiral_restr0.0640.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02385
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5542.351151
X-RAY DIFFRACTIONr_mcbond_other5.5562.3481150
X-RAY DIFFRACTIONr_mcangle_it7.2223.4691423
X-RAY DIFFRACTIONr_mcangle_other7.2193.4711424
X-RAY DIFFRACTIONr_scbond_it7.5413.0341135
X-RAY DIFFRACTIONr_scbond_other7.543.0391136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.2734.2331661
X-RAY DIFFRACTIONr_long_range_B_refined11.69528.1892251
X-RAY DIFFRACTIONr_long_range_B_other11.69428.2182252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 104 -
Rwork0.348 1027 -
all-1131 -
obs--95.52 %
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)
119.3332-7.93270.64484.6462-0.24360.601-0.4042-0.89020.17140.52340.2685-0.2122-0.09950.12260.13580.2413-0.0580.00110.15460.03230.164-6.8792.15621.449
27.54190.9528-1.37611.2964-0.38751.72470.06020.3471-0.1566-0.1471-0.1034-0.06970.07480.07490.04310.1329-0.0141-0.02230.10120.00590.0652.01511.08510.764
33.8760.7069-1.43393.5305-0.1523.35450.06210.16890.21-0.19220.03970.0677-0.04040.1111-0.10170.1440.0345-0.04420.09610.00890.047-4.697.8746.614
414.46926.1433-11.60116.4261-8.335116.7286-0.1420.51820.1331-0.36960.15580.19290.191-0.0949-0.01370.17420.0235-0.03270.1261-0.03210.1326-5.20110.6951.379
53.42320.3649-0.02535.21630.98344.04170.03990.0886-0.1127-0.1217-0.03630.06840.09-0.1007-0.00350.0918-0-0.00640.11760.01970.0927-4.9681.9814.431
64.12521.42240.97791.95470.41994.349-0.1587-0.22620.40290.42770.1104-0.0252-0.1387-0.04690.04830.22050.013-0.04720.17530.01420.15660.4312.0315.983
77.0615-0.2044-1.69694.4791-1.35943.1473-0.1882-0.76730.14490.6460.1617-0.11820.06410.1540.02660.23210.0238-0.02570.0939-0.00050.10079.6088.40720.051
818.6648-7.32212.440213.28121.69263.9542-0.2760.15950.5052-0.15460.07360.103-0.5831-0.29090.20230.1912-0.03010.04430.16820.01330.14123.18121.1379.508
92.72030.6019-0.32292.6184-0.15561.3410.01880.0404-0.0023-0.0061-0.00070.0661-0.0142-0.0729-0.01820.10960.006-0.00470.09420.00010.048528.54920.68811.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 14
2X-RAY DIFFRACTION2A15 - 32
3X-RAY DIFFRACTION3A33 - 54
4X-RAY DIFFRACTION4A55 - 69
5X-RAY DIFFRACTION5A70 - 107
6X-RAY DIFFRACTION6A108 - 133
7X-RAY DIFFRACTION7A134 - 147
8X-RAY DIFFRACTION8A148 - 160
9X-RAY DIFFRACTION9B5 - 157

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