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- PDB-6fxb: Bovine beta-lactoglobulin variant A at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 6fxb
TitleBovine beta-lactoglobulin variant A at pH 4.0
ComponentsMajor allergen beta-lactoglobulin
KeywordsALLERGEN / lactoglobulin / milk protein
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
NITRATE ION / DI(HYDROXYETHYL)ETHER / Major allergen beta-lactoglobulin / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKhan, S. / Ipsen, R. / Almdal, K. / Svensson, B. / Harris, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Research Council for Independent Research | Technical and Production SciencesHEXPIN Denmark
CitationJournal: Biomacromolecules / Year: 2018
Title: Revealing the Dimeric Crystal and Solution Structure of beta-Lactoglobulin at pH 4 and Its pH and Salt Dependent Monomer-Dimer Equilibrium.
Authors: Khan, S. / Ipsen, R. / Almdal, K. / Svensson, B. / Harris, P.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_remark / pdbx_data_processing_status ...database_PDB_remark / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_PDB_remark.text
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)73,7797
Polymers73,5494
Non-polymers2303
Water3,369187
1
A: Major allergen beta-lactoglobulin
B: Major allergen beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8994
Polymers36,7752
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Major allergen beta-lactoglobulin
D: Major allergen beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8813
Polymers36,7752
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.110, 75.610, 140.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 and (name N or name...
21(chain B and ((resid 2 and (name N or name...
31(chain C and ((resid 2 and (name N or name...
41(chain D and ((resid 2 and (name O or name...

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILE(chain A and ((resid 2 and (name N or name...AA22
12LEULEU(chain A and ((resid 2 and (name N or name...AA1 - 1621 - 162
13LEULEU(chain A and ((resid 2 and (name N or name...AA1 - 1621 - 162
14LEULEU(chain A and ((resid 2 and (name N or name...AA1 - 1621 - 162
15LEULEU(chain A and ((resid 2 and (name N or name...AA1 - 1621 - 162
16LEULEU(chain A and ((resid 2 and (name N or name...AA1 - 1621 - 162
17LEULEU(chain A and ((resid 2 and (name N or name...AA1 - 1621 - 162
21ILEILE(chain B and ((resid 2 and (name N or name...BB22
22LEULEU(chain B and ((resid 2 and (name N or name...BB1 - 1621 - 162
23LEULEU(chain B and ((resid 2 and (name N or name...BB1 - 1621 - 162
24LEULEU(chain B and ((resid 2 and (name N or name...BB1 - 1621 - 162
25LEULEU(chain B and ((resid 2 and (name N or name...BB1 - 1621 - 162
26LEULEU(chain B and ((resid 2 and (name N or name...BB1 - 1621 - 162
27LEULEU(chain B and ((resid 2 and (name N or name...BB1 - 1621 - 162
31ILEILE(chain C and ((resid 2 and (name N or name...CC22
32LEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1621 - 162
33LEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1621 - 162
34LEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1621 - 162
35LEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1621 - 162
36LEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1621 - 162
37LEULEU(chain C and ((resid 2 and (name N or name...CC1 - 1621 - 162
41ILEILE(chain D and ((resid 2 and (name O or name...DD22
42LEULEU(chain D and ((resid 2 and (name O or name...DD1 - 1621 - 162
43LEULEU(chain D and ((resid 2 and (name O or name...DD1 - 1621 - 162
44LEULEU(chain D and ((resid 2 and (name O or name...DD1 - 1621 - 162
45LEULEU(chain D and ((resid 2 and (name O or name...DD1 - 1621 - 162
46LEULEU(chain D and ((resid 2 and (name O or name...DD1 - 1621 - 162
47LEULEU(chain D and ((resid 2 and (name O or name...DD1 - 1621 - 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 natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: B5B0D4, UniProt: P02754*PLUS
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: BLGA (15 mg/ml) in 50 mM sodium citrate/citric acid pH 4.0 2 ul BLGA and 2 ul 12% PEG 4000, 150 mM magnesium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.99→60.566 Å / Num. obs: 46190 / % possible obs: 92.5 % / Redundancy: 4.291 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.073 / Χ2: 0.998 / Net I/σ(I): 11.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.043.7440.5292.6733970.8650.60993.6
2.04-2.13.8840.4273.233110.9290.48793.2
2.1-2.163.9680.3173.9932120.9520.36193.4
2.16-2.223.860.2524.7731110.9710.28892.8
2.22-2.33.9440.2165.6529970.9780.24691.6
2.3-2.384.3790.1716.8328760.9870.19292.1
2.38-2.474.5540.1458.0429250.9910.16295.1
2.47-2.574.5990.1259.7127860.9920.13895.2
2.57-2.684.6290.10811.3226600.9940.1294.4
2.68-2.814.6180.09312.825640.9940.10394.4
2.81-2.974.5190.08214.8824120.9940.09194.3
2.97-3.154.290.07116.6723000.9950.07993.3
3.15-3.364.1930.06718.7920650.9960.07590
3.36-3.634.5960.0621.3919670.9950.06791.5
3.63-3.984.7110.05822.8918230.9950.06591.4
3.98-4.454.6350.05423.5316550.9970.0691
4.45-5.144.5810.05223.7114330.9970.05789.2
5.14-6.294.20.05422.2412070.9950.06187.3
6.29-8.94.5780.04723.79430.9970.05386.8
8.9-60.5664.5880.04623.955460.9970.05181.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→60.566 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 29.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 2267 4.94 %
Rwork0.2321 43629 -
obs0.234 45896 93.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.29 Å2 / Biso mean: 41.0041 Å2 / Biso min: 12.52 Å2
Refinement stepCycle: final / Resolution: 2→60.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 15 187 5346
Biso mean--51.42 42.71 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055248
X-RAY DIFFRACTIONf_angle_d0.8387111
X-RAY DIFFRACTIONf_chiral_restr0.055836
X-RAY DIFFRACTIONf_plane_restr0.005906
X-RAY DIFFRACTIONf_dihedral_angle_d13.6893307
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2654X-RAY DIFFRACTION11.029TORSIONAL
12B2654X-RAY DIFFRACTION11.029TORSIONAL
13C2654X-RAY DIFFRACTION11.029TORSIONAL
14D2654X-RAY DIFFRACTION11.029TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.04350.37871350.32112786292196
2.0435-2.0910.35051510.29632717286895
2.091-2.14330.31581670.2622724289196
2.1433-2.20130.3171410.2522757289895
2.2013-2.26610.28871380.23782690282894
2.2661-2.33920.26351470.21712627277491
2.3392-2.42280.30031390.22122750288995
2.4228-2.51980.31641270.22692802292996
2.5198-2.63450.31591260.23072748287496
2.6345-2.77340.341350.23742772290795
2.7734-2.94720.3051360.23912760289694
2.9472-3.17470.291520.22992718287093
3.1747-3.49420.2651440.22172634277890
3.4942-3.99970.24991400.22282734287492
3.9997-5.03880.20721490.20222684283390
5.0388-60.59390.2391400.24712726286687

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