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- PDB-5nuk: Engineered beta-lactoglobulin: variant I56F-L39A-M107F in complex... -

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Basic information

Entry
Database: PDB / ID: 5nuk
TitleEngineered beta-lactoglobulin: variant I56F-L39A-M107F in complex with chlorpromazine (LG-FAF-CLP)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / beta-lactoglobulin / lipocalin / mutation / chlorpromazine / complex
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
PHOSPHATE ION / Chem-Z80 / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLoch, J.I. / Bonarek, P. / Tworzydlo, M. / Lazinska, 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 / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed
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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8786
Polymers18,2411
Non-polymers6375
Water1,892105
1
A: Beta-lactoglobulin
hetero molecules

A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,75712
Polymers36,4822
Non-polymers1,27510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2240 Å2
ΔGint-54 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.160, 53.160, 112.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-204-

PO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18240.930 Da / Num. of mol.: 1 / Mutation: L1A, I2S, I56F, L39A, M107F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: LGB / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P02754

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Non-polymers , 6 types, 110 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.80 M (NH4)2SO4, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→14.81 Å / Num. obs: 20925 / % possible obs: 99.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 10.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1116 / % possible all: 99.4

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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: 1.7→14.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.809 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26864 2039 9.8 %RANDOM
Rwork0.21476 ---
obs0.22007 18857 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.376 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→14.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 38 105 1373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021317
X-RAY DIFFRACTIONr_bond_other_d0.0030.021291
X-RAY DIFFRACTIONr_angle_refined_deg1.4412.0171786
X-RAY DIFFRACTIONr_angle_other_deg0.8063.0042994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53426.07156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28415249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.734154
X-RAY DIFFRACTIONr_chiral_restr0.0950.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211433
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02267
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_it1.7542.368625
X-RAY DIFFRACTIONr_mcbond_other1.7542.368624
X-RAY DIFFRACTIONr_mcangle_it2.8263.54781
X-RAY DIFFRACTIONr_mcangle_other2.8253.541782
X-RAY DIFFRACTIONr_scbond_it2.182.762690
X-RAY DIFFRACTIONr_scbond_other2.1852.753686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5424.005996
X-RAY DIFFRACTIONr_long_range_B_refined5.74220.1751503
X-RAY DIFFRACTIONr_long_range_B_other5.74420.1721503
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 130 -
Rwork0.317 1359 -
obs--99.27 %

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