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- PDB-7q2p: Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with d... -

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Basic information

Entry
Database: PDB / ID: 7q2p
TitleBeta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#2)
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / lactoglobulin / mutation / desipramine
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 / Lipocalin signature.
Similarity search - Domain/homology
Chem-DSM / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 25, 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 / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-lactoglobulin
BBB: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,74611
Polymers36,5602
Non-polymers1,1869
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-19 kcal/mol
Surface area15040 Å2
Unit cell
Length a, b, c (Å)55.814, 70.517, 178.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11BBB-450-

HOH

21BBB-469-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 9 - 162 / Label seq-ID: 9 - 162

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18279.965 Da / Num. of mol.: 2 / Mutation: L1A, I2S, L39A, I56F, M107W
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 (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P02754

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Non-polymers , 5 types, 177 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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.: 3 / Source method: obtained synthetically / Formula: C18H22N2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 48.88 %
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

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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: 1.688→45.519 Å / Num. obs: 39985 / % possible obs: 99.6 % / Redundancy: 12.94 % / CC1/2: 1 / Rrim(I) all: 0.072 / Net I/σ(I): 19.43
Reflection shellResolution: 1.69→1.79 Å / Num. unique obs: 6354 / CC1/2: 0.857 / Rrim(I) all: 1.68

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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: 1.69→45.519 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.646 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.106 / Details: Hydrogen atoms were added at riding positions
RfactorNum. reflection% reflection
Rfree0.2355 1000 2.501 %
Rwork0.1892 38980 -
all0.19 --
obs-39980 99.577 %
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: 43.721 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å2-0 Å2
2--5.119 Å2-0 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.69→45.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 80 168 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132593
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172507
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6453512
X-RAY DIFFRACTIONr_angle_other_deg1.4921.6195811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27325.47117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26615467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.785156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023020
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
X-RAY DIFFRACTIONr_nbd_refined0.1940.2404
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.22219
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21182
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.216
X-RAY DIFFRACTIONr_nbd_other0.2070.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.220
X-RAY DIFFRACTIONr_mcbond_it8.4863.2881235
X-RAY DIFFRACTIONr_mcbond_other8.3913.2841234
X-RAY DIFFRACTIONr_mcangle_it8.9774.8761539
X-RAY DIFFRACTIONr_mcangle_other8.9884.8811540
X-RAY DIFFRACTIONr_scbond_it14.4244.3591358
X-RAY DIFFRACTIONr_scbond_other13.7934.3391351
X-RAY DIFFRACTIONr_scangle_it17.4026.081972
X-RAY DIFFRACTIONr_scangle_other16.4996.0381961
X-RAY DIFFRACTIONr_lrange_it17.11240.5772660
X-RAY DIFFRACTIONr_lrange_other17.15640.3312641
X-RAY DIFFRACTIONr_ncsr_local_group_10.1580.054231
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.158330.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.158330.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.7320.339720.4512824X-RAY DIFFRACTION99.2461
1.732-1.7790.478710.4162766X-RAY DIFFRACTION99.4044
1.779-1.8310.355690.352688X-RAY DIFFRACTION99.4589
1.831-1.8870.313670.3162634X-RAY DIFFRACTION99.8891
1.887-1.9490.309650.2922532X-RAY DIFFRACTION99.5401
1.949-2.0170.258640.2392490X-RAY DIFFRACTION100
2.017-2.0930.214610.2012380X-RAY DIFFRACTION100
2.093-2.1780.275590.1842277X-RAY DIFFRACTION99.3197
2.178-2.2750.238570.192212X-RAY DIFFRACTION99.3868
2.275-2.3860.17530.1592104X-RAY DIFFRACTION100
2.386-2.5140.253520.1642019X-RAY DIFFRACTION99.9035
2.514-2.6660.274500.1761923X-RAY DIFFRACTION99.8987
2.666-2.850.222450.1671777X-RAY DIFFRACTION98.6999
2.85-3.0770.274430.1691682X-RAY DIFFRACTION100
3.077-3.3690.269400.1791564X-RAY DIFFRACTION100
3.369-3.7640.2370.1651424X-RAY DIFFRACTION99.727
3.764-4.3420.192320.1471237X-RAY DIFFRACTION98.6781
4.342-5.3060.171270.1331079X-RAY DIFFRACTION99.9097
5.306-7.4530.312220.21858X-RAY DIFFRACTION99.6602
7.453-45.5190.168140.206510X-RAY DIFFRACTION97.2171
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)
11.4233-0.1516-0.27760.0720.16550.42060.00740.09-0.15560.00080.0152-0-0.01610.0276-0.02260.0180.0179-0.0080.0557-0.04050.056716.4439-1.045161.8954
21.4126-0.02530.07970.08030.26210.95620.0121-0.0456-0.0632-0.0169-0.0267-0.0032-0.0488-0.02350.01460.00830.0159-0.00920.05630.00220.051345.15593.211774.231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA4 - 162
2X-RAY DIFFRACTION1ALLAaA501
3X-RAY DIFFRACTION1ALLAbA705
4X-RAY DIFFRACTION2ALLBBB9 - 162
5X-RAY DIFFRACTION2ALLBaB301

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