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- PDB-5nun: Engineered beta-lactoglobulin: variant F105L-L39A-M107F in comple... -

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Basic information

Entry
Database: PDB / ID: 5nun
TitleEngineered beta-lactoglobulin: variant F105L-L39A-M107F in complex with chlorpromazine (LG-LAF-CLP)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / beta-lactoglobulin / lipocalin / complex / 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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-Z80 / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLoch, J.I. / Bonarek, P. / Towrzydlo, M. / Lazinskia, I. / Szydlowska, J. / Lewinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2012/05/B/ST5/00278 Poland
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: The engineered beta-lactoglobulin with complementarity to the chlorpromazine chiral conformers.
Authors: Loch, J.I. / Bonarek, P. / Tworzydlo, M. / Lazinska, I. / Szydlowska, J. / Lipowska, J. / Rzesikowska, K. / Lewinski, K.
History
DepositionApr 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Dec 7, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4922
Polymers18,1731
Non-polymers3191
Water1,35175
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9844
Polymers36,3462
Non-polymers6382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)53.657, 53.657, 110.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18172.896 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39a, F105L, M107F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic 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-Z80 / 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine / Chlorpromazine


Mass: 318.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19ClN2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.40 M (NH4)2SO4 in 0.1 M Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→13.84 Å / Num. obs: 13945 / % possible obs: 99.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 6.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2 / Num. unique obs: 1043 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 1.95→13.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.994 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26222 1356 9.7 %RANDOM
Rwork0.21455 ---
obs0.21948 12566 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.984 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.95→13.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 21 75 1347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021364
X-RAY DIFFRACTIONr_bond_other_d0.0010.021324
X-RAY DIFFRACTIONr_angle_refined_deg1.7272.0231858
X-RAY DIFFRACTIONr_angle_other_deg0.8483.0093073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.71326.94959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21615252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.55153
X-RAY DIFFRACTIONr_chiral_restr0.1110.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
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_it2.32.716654
X-RAY DIFFRACTIONr_mcbond_other2.292.714653
X-RAY DIFFRACTIONr_mcangle_it3.564.063822
X-RAY DIFFRACTIONr_mcangle_other3.5594.064823
X-RAY DIFFRACTIONr_scbond_it2.6823.158709
X-RAY DIFFRACTIONr_scbond_other2.683.161710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.294.5881034
X-RAY DIFFRACTIONr_long_range_B_refined6.5422.4621467
X-RAY DIFFRACTIONr_long_range_B_other6.48322.3981451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 88 -
Rwork0.28 899 -
obs--98.01 %

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