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- PDB-6rwq: Engineered beta-lactoglobulin: variant F105L in complex with myri... -

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Basic information

Entry
Database: PDB / ID: 6rwq
TitleEngineered beta-lactoglobulin: variant F105L in complex with myristic acid
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / Lipocalin / mutation
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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
DepositionJun 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)18,4893
Polymers18,1991
Non-polymers2902
Water1,838102
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9796
Polymers36,3982
Non-polymers5814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)53.071, 53.071, 112.126
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: 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 (E. coli) / Variant (production host): Origami B (DE3) / References: UniProt: P02754
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→14.18 Å / Num. obs: 11972 / % possible obs: 99.5 % / Redundancy: 2.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.055 / Rrim(I) all: 0.101 / Net I/σ(I): 6.6 / Num. measured all: 31794 / Scaling rejects: 15
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
2.05-2.1120.215209910290.9050.190.2882.299.6
8.45-14.182.30.1133611550.8950.0880.14512.875.6

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 2.05→14.18 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.48 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.192
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1266 10.6 %RANDOM
Rwork0.1906 ---
obs0.1974 10681 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.23 Å2 / Biso mean: 35.605 Å2 / Biso min: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 2.05→14.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 20 102 1326
Biso mean--51.05 36.8 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171197
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.6661677
X-RAY DIFFRACTIONr_angle_other_deg0.8531.6752805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37125.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53415231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.798153
X-RAY DIFFRACTIONr_chiral_restr0.0630.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02195
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_it2.3951.159614
X-RAY DIFFRACTIONr_mcbond_other2.3921.158613
X-RAY DIFFRACTIONr_mcangle_it3.3051.723764
X-RAY DIFFRACTIONr_mcangle_other3.3031.723765
X-RAY DIFFRACTIONr_scbond_it4.7981.7626
X-RAY DIFFRACTIONr_scbond_other4.7541.701626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6222.307913
X-RAY DIFFRACTIONr_long_range_B_refined8.48515.5841307
X-RAY DIFFRACTIONr_long_range_B_other8.45415.1911293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.102 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 84 -
Rwork0.23 760 -
all-844 -
obs--99.06 %
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)
12.1275-3.1728-0.753311.84280.63681.9542-0.15470.1735-0.07690.01580.0101-0.41060.141-0.16580.14460.22330.0442-0.09330.1737-0.09990.1259-15.688-18.425-22.537
22.5223-1.2479-0.61720.72820.02354.31440.0616-0.11950.2119-0.0865-0.0557-0.0479-0.20620.4048-0.00590.1829-0.0011-0.04220.1887-0.01620.1115-7.549-7.241-8.443
33.4837-0.08661.87245.50013.89099.30920.26050.33970.4015-0.4532-0.1385-0.2043-0.94690.0913-0.1220.31610.0209-0.00050.12640.0680.1291-10.706-1.435-20.251
46.79983.1399-0.613427.5080.79043.58480.13760.7117-0.147-0.8352-0.1312-0.4811-0.10890.3052-0.00640.27760.072-0.03170.2578-0.02560.0295-7.243-15.278-28.531
521.50828.0056-0.28155.3006-3.38784.6895-0.55590.567-0.171-0.2966-0.0482-0.49670.00610.48140.60410.621-0.20410.0190.5604-0.04440.16080.313-11.793-22.94
64.7219-1.98830.93892.12581.8934.5907-0.03810.0393-0.2283-0.0711-0.10830.25090.11320.03010.14640.30110.0743-0.05890.2206-0.03450.1338-13.467-16.295-15.819
74.4463-3.3488-0.67694.71491.92622.7827-0.1665-0.2415-0.46790.3019-0.01970.51120.3079-0.31640.18630.1926-0.009-0.01930.16080.00550.1545-19.6-15.71-8.446
85.1042-3.2704-0.08632.94030.57363.915-0.0946-0.4392-0.0563-0.08340.05460.1445-0.12860.05220.04010.23770.0275-0.05390.2012-0.00410.1086-12.707-8.352-4.883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 18
2X-RAY DIFFRACTION2A19 - 43
3X-RAY DIFFRACTION3A44 - 71
4X-RAY DIFFRACTION4A72 - 83
5X-RAY DIFFRACTION5A84 - 93
6X-RAY DIFFRACTION6A94 - 121
7X-RAY DIFFRACTION7A122 - 140
8X-RAY DIFFRACTION8A141 - 162

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