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- PDB-7er3: Crystal structure of beta-lactoglobulin complexed with chloroquine -

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Basic information

Entry
Database: PDB / ID: 7er3
TitleCrystal structure of beta-lactoglobulin complexed with chloroquine
ComponentsMajor allergen beta-lactoglobulin
KeywordsIMMUNE SYSTEM / beta-lactoglobulin / chloroquine
Function / homology
Function and homology information


retinol binding / extracellular region
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-0TX / Major allergen beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsYao, Q. / Ma, J. / Xing, Y. / Zang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Binding of Chloroquine to Whey Protein Relieves Its Cytotoxicity while Enhancing Its Uptake by Cells.
Authors: Yao, Q. / Xing, Y. / Ma, J. / Wang, C. / Zang, J. / Zhao, G.
History
DepositionMay 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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

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Assembly

Deposited unit
A: Major allergen beta-lactoglobulin
B: Major allergen beta-lactoglobulin
C: Major allergen beta-lactoglobulin
D: Major allergen beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8298
Polymers73,5494
Non-polymers1,2794
Water41423
1
A: Major allergen beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7072
Polymers18,3871
Non-polymers3201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major allergen beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7072
Polymers18,3871
Non-polymers3201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Major allergen beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7072
Polymers18,3871
Non-polymers3201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Major allergen beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7072
Polymers18,3871
Non-polymers3201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.118, 66.953, 78.044
Angle α, β, γ (deg.)90.000, 111.740, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:4 or resseq 6:7 or resseq...
21(chain B and (resseq 1:4 or resseq 6:7 or resseq...
31(chain C and (resseq 1:4 or resseq 6:7 or resseq...
41(chain D and (resseq 1:4 or resseq 6:7 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 4
121(chain A and (resseq 1:4 or resseq 6:7 or resseq...A6 - 7
131(chain A and (resseq 1:4 or resseq 6:7 or resseq...A9 - 12
141(chain A and (resseq 1:4 or resseq 6:7 or resseq...A0
151(chain A and (resseq 1:4 or resseq 6:7 or resseq...A46
161(chain A and (resseq 1:4 or resseq 6:7 or resseq...A65 - 68
171(chain A and (resseq 1:4 or resseq 6:7 or resseq...A72
181(chain A and (resseq 1:4 or resseq 6:7 or resseq...A78 - 8
191(chain A and (resseq 1:4 or resseq 6:7 or resseq...A85 - 86
1101(chain A and (resseq 1:4 or resseq 6:7 or resseq...A88 - 89
1111(chain A and (resseq 1:4 or resseq 6:7 or resseq...A92 - 9
1121(chain A and (resseq 1:4 or resseq 6:7 or resseq...A92 - 1
1131(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1141(chain A and (resseq 1:4 or resseq 6:7 or resseq...A129 - 133
1151(chain A and (resseq 1:4 or resseq 6:7 or resseq...A139
1161(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1171(chain A and (resseq 1:4 or resseq 6:7 or resseq...A146
1181(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1191(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1201(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1211(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1221(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1231(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1241(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1251(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1261(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1271(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1281(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1291(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
1301(chain A and (resseq 1:4 or resseq 6:7 or resseq...A1 - 162
211(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 4
221(chain B and (resseq 1:4 or resseq 6:7 or resseq...B6 - 7
231(chain B and (resseq 1:4 or resseq 6:7 or resseq...B9 - 12
241(chain B and (resseq 1:4 or resseq 6:7 or resseq...B14 - 28
251(chain B and (resseq 1:4 or resseq 6:7 or resseq...B0
261(chain B and (resseq 1:4 or resseq 6:7 or resseq...B48 - 162
271(chain B and (resseq 1:4 or resseq 6:7 or resseq...B46562
281(chain B and (resseq 1:4 or resseq 6:7 or resseq...B62 - 68
291(chain B and (resseq 1:4 or resseq 6:7 or resseq...B82 - 73
2101(chain B and (resseq 1:4 or resseq 6:7 or resseq...B76
2111(chain B and (resseq 1:4 or resseq 6:7 or resseq...B7
2121(chain B and (resseq 1:4 or resseq 6:7 or resseq...B88 - 86
2131(chain B and (resseq 1:4 or resseq 6:7 or resseq...B82 - 89
2141(chain B and (resseq 1:4 or resseq 6:7 or resseq...B90 - 99
2151(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2161(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2171(chain B and (resseq 1:4 or resseq 6:7 or resseq...B114 - 126
2181(chain B and (resseq 1:4 or resseq 6:7 or resseq...B142 - 145
2191(chain B and (resseq 1:4 or resseq 6:7 or resseq...B146
2201(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2211(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2221(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2231(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2241(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2251(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2261(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2271(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2281(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2291(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
2301(chain B and (resseq 1:4 or resseq 6:7 or resseq...B1 - 162
311(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 4
321(chain C and (resseq 1:4 or resseq 6:7 or resseq...C6 - 7
331(chain C and (resseq 1:4 or resseq 6:7 or resseq...C9 - 12
341(chain C and (resseq 1:4 or resseq 6:7 or resseq...C14 - 28
351(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
361(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
371(chain C and (resseq 1:4 or resseq 6:7 or resseq...C6562
381(chain C and (resseq 1:4 or resseq 6:7 or resseq...C65 - 68
391(chain C and (resseq 1:4 or resseq 6:7 or resseq...C72 - 73
3101(chain C and (resseq 1:4 or resseq 6:7 or resseq...C85 - 86
3111(chain C and (resseq 1:4 or resseq 6:7 or resseq...C88 - 86
3121(chain C and (resseq 1:4 or resseq 6:7 or resseq...C88 - 89
3131(chain C and (resseq 1:4 or resseq 6:7 or resseq...C102 - 107
3141(chain C and (resseq 1:4 or resseq 6:7 or resseq...C114 - 126
3151(chain C and (resseq 1:4 or resseq 6:7 or resseq...C129 - 133
3161(chain C and (resseq 1:4 or resseq 6:7 or resseq...C136 - 137
3171(chain C and (resseq 1:4 or resseq 6:7 or resseq...C139
3181(chain C and (resseq 1:4 or resseq 6:7 or resseq...C142 - 145
3191(chain C and (resseq 1:4 or resseq 6:7 or resseq...C146
3201(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3211(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3221(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3231(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3241(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3251(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3261(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3271(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3281(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3291(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3301(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
3311(chain C and (resseq 1:4 or resseq 6:7 or resseq...C1 - 162
411(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 4
421(chain D and (resseq 1:4 or resseq 6:7 or resseq...D6 - 7
431(chain D and (resseq 1:4 or resseq 6:7 or resseq...D9 - 12
441(chain D and (resseq 1:4 or resseq 6:7 or resseq...D0
451(chain D and (resseq 1:4 or resseq 6:7 or resseq...D46
461(chain D and (resseq 1:4 or resseq 6:7 or resseq...D65 - 68
471(chain D and (resseq 1:4 or resseq 6:7 or resseq...D72
481(chain D and (resseq 1:4 or resseq 6:7 or resseq...D78 - 8
491(chain D and (resseq 1:4 or resseq 6:7 or resseq...D85 - 86
4101(chain D and (resseq 1:4 or resseq 6:7 or resseq...D88 - 89
4111(chain D and (resseq 1:4 or resseq 6:7 or resseq...D92 - 9
4121(chain D and (resseq 1:4 or resseq 6:7 or resseq...D92 - 1
4131(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4141(chain D and (resseq 1:4 or resseq 6:7 or resseq...D129 - 133
4151(chain D and (resseq 1:4 or resseq 6:7 or resseq...D139
4161(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4171(chain D and (resseq 1:4 or resseq 6:7 or resseq...D146
4181(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4191(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4201(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4211(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4221(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4231(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4241(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4251(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4261(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4271(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4281(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4291(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162
4301(chain D and (resseq 1:4 or resseq 6:7 or resseq...D1 - 162

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Components

#1: Protein
Major allergen beta-lactoglobulin


Mass: 18387.264 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: B5B0D4
#2: Chemical
ChemComp-0TX / (4S)-N~4~-(7-chloroquinolin-4-yl)-N~1~,N~1~-diethylpentane-1,4-diamine


Mass: 319.872 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H26ClN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 293 K / Method: evaporation, recrystallization
Details: 1000 mM Sodium citrate tribasic, 100 mM Tris-HCl (pH 7.0) and 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.598→29.595 Å / Num. obs: 21922 / % possible obs: 98 % / Redundancy: 1.8 % / CC1/2: 0.961 / Net I/σ(I): 6.1
Reflection shellResolution: 2.598→2.691 Å / Num. unique obs: 21922 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-30003.27data reduction
HKL-3000data scaling
PHENIXmodel building
PHENIXv1.10.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IO6

5io6


Resolution: 2.598→29.595 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 41.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3244 1098 5.02 %
Rwork0.2472 --
obs0.2514 21862 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.76 Å2 / Biso mean: 66.8453 Å2 / Biso min: 14.57 Å2
Refinement stepCycle: final / Resolution: 2.598→29.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 192 23 5359
Biso mean--88.57 45.97 -
Num. residues----648
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2652X-RAY DIFFRACTION19.072TORSIONAL
12B2652X-RAY DIFFRACTION19.072TORSIONAL
13C2652X-RAY DIFFRACTION19.072TORSIONAL
14D2652X-RAY DIFFRACTION19.072TORSIONAL
LS refinement shellResolution: 2.5976→2.7157 Å
RfactorNum. reflection% reflection
Rfree0.3957 117 -
Rwork0.2865 --
obs-2299 87 %

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