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- PDB-7q19: Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with d... -

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Basic information

Entry
Database: PDB / ID: 7q19
TitleBeta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#3)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / mutation / desipramine
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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Chem-DSM / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLoch, J.I. / Barciszewski, J. / Pokrywka, K. / Lewinski, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2022
Title: New ligand-binding sites identified in the crystal structures of [beta]-lactoglobulin complexes with desipramine
Authors: Loch, J.I. / Barciszewski, J. / Sliwiak, J. / Bonarek, P. / Wrobel, P. / Pokrywka, K. / Shabalin, I.G. / Minor, W. / Jaskolski, M. / Lewinski, K.
History
DepositionOct 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9078
Polymers18,2801
Non-polymers6277
Water2,162120
1
AAA: Beta-lactoglobulin
hetero molecules

AAA: Beta-lactoglobulin
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 37.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)37,81416
Polymers36,5602
Non-polymers1,25414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area2770 Å2
ΔGint-73 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.298, 66.298, 60.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11AAA-203-

SO4

21AAA-204-

SO4

31AAA-204-

SO4

41AAA-390-

HOH

51AAA-406-

HOH

61AAA-420-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18279.965 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39A, I56F, M107W
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

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Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-DSM / 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE / Desipramine;Norpramin


Mass: 266.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant, inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.40 M (NH4)2SO4, 0.5 M Tris-HCl pH 8.5, desipramine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→41.69 Å / Num. obs: 22796 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 1 / Rrim(I) all: 0.051 / Net I/σ(I): 23.24
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 9.11 % / Mean I/σ(I) obs: 1.98 / Num. unique obs: 3482 / CC1/2: 0.087 / Rrim(I) all: 1.022 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BSY

1bsy


Resolution: 1.55→41.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.015 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.094
RfactorNum. reflection% reflection
Rfree0.2337 1000 4.387 %
Rwork0.1971 21796 -
all0.199 --
obs-22796 99.917 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.512 Å20.256 Å2-0 Å2
2--0.512 Å2-0 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 37 120 1411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161277
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.6451799
X-RAY DIFFRACTIONr_angle_other_deg1.3851.6072968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60625.73861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.015153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
X-RAY DIFFRACTIONr_nbd_refined0.1960.2217
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21140
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2611
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.217
X-RAY DIFFRACTIONr_nbd_other0.2020.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.218
X-RAY DIFFRACTIONr_mcbond_it1.6322.279634
X-RAY DIFFRACTIONr_mcbond_other1.6332.278633
X-RAY DIFFRACTIONr_mcangle_it2.6593.417792
X-RAY DIFFRACTIONr_mcangle_other2.6573.419793
X-RAY DIFFRACTIONr_scbond_it2.3092.649692
X-RAY DIFFRACTIONr_scbond_other2.322.618685
X-RAY DIFFRACTIONr_scangle_it3.6393.8511004
X-RAY DIFFRACTIONr_scangle_other3.6583.801993
X-RAY DIFFRACTIONr_lrange_it6.16927.9781401
X-RAY DIFFRACTIONr_lrange_other6.16527.4851381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.5890.288710.2731566X-RAY DIFFRACTION99.2723
1.589-1.6330.313710.2451543X-RAY DIFFRACTION99.8762
1.633-1.680.291680.2331487X-RAY DIFFRACTION100
1.68-1.7320.295690.2151501X-RAY DIFFRACTION100
1.732-1.7890.288650.2181411X-RAY DIFFRACTION99.8647
1.789-1.8510.265630.21366X-RAY DIFFRACTION100
1.851-1.9210.202600.191322X-RAY DIFFRACTION100
1.921-1.9990.219600.191305X-RAY DIFFRACTION100
1.999-2.0880.273570.2011234X-RAY DIFFRACTION100
2.088-2.1890.261530.191156X-RAY DIFFRACTION100
2.189-2.3080.232520.1971141X-RAY DIFFRACTION100
2.308-2.4470.214490.2061070X-RAY DIFFRACTION100
2.447-2.6150.286460.209998X-RAY DIFFRACTION100
2.615-2.8240.22430.22932X-RAY DIFFRACTION100
2.824-3.0920.32400.207885X-RAY DIFFRACTION100
3.092-3.4550.206370.185788X-RAY DIFFRACTION100
3.455-3.9850.22320.182698X-RAY DIFFRACTION100
3.985-4.8690.184270.158608X-RAY DIFFRACTION99.8428
4.869-6.8390.17230.218489X-RAY DIFFRACTION100
6.839-41.6890.279140.193296X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.8202 Å / Origin y: 52.1562 Å / Origin z: 15.2609 Å
111213212223313233
T0.0758 Å20.032 Å2-0.0093 Å2-0.0267 Å20.0117 Å2--0.03 Å2
L0.2489 °20.3581 °20.0644 °2-0.7209 °20.3262 °2--0.9186 °2
S-0.0708 Å °-0.0298 Å °-0.0334 Å °-0.0946 Å °0.0096 Å °0.0049 Å °-0.1226 Å °-0.0248 Å °0.0612 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA4 - 161
2X-RAY DIFFRACTION1ALLAAA201

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