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- PDB-7lwc: Goat beta-lactoglobulin mutant Q59A -

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Basic information

Entry
Database: PDB / ID: 7lwc
TitleGoat beta-lactoglobulin mutant Q59A
ComponentsBeta-lactoglobulin
KeywordsLIPID TRANSPORT
Function / homology
Function and homology information


retinol 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
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMunoz, D.A. / Dobson, R.C.J.
CitationJournal: To Be Published
Title: Engineering food proteins for improved digestibility and lower allergenicity: a case study using caprine beta-lactoglobulin
Authors: Munoz, D.A.
History
DepositionFeb 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
B: Beta-lactoglobulin


Theoretical massNumber of molelcules
Total (without water)36,3102
Polymers36,3102
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.234, 58.155, 144.246
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 7 through 11 or resid 14...
21(chain B and (resid 7 through 11 or resid 14...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 through 11 or resid 14...A7 - 11
121(chain A and (resid 7 through 11 or resid 14...A14 - 32
131(chain A and (resid 7 through 11 or resid 14...A34 - 38
141(chain A and (resid 7 through 11 or resid 14...A4 - 52
151(chain A and (resid 7 through 11 or resid 14...A54 - 56
161(chain A and (resid 7 through 11 or resid 14...A60 - 67
171(chain A and (resid 7 through 11 or resid 14...A69 - 71
181(chain A and (resid 7 through 11 or resid 14...A73 - 90
191(chain A and (resid 7 through 11 or resid 14...A4 - 160
1101(chain A and (resid 7 through 11 or resid 14...A91 - 106
1111(chain A and (resid 7 through 11 or resid 14...A0
1121(chain A and (resid 7 through 11 or resid 14...A4 - 160
1131(chain A and (resid 7 through 11 or resid 14...A4 - 160
1141(chain A and (resid 7 through 11 or resid 14...A141 - 144
1151(chain A and (resid 7 through 11 or resid 14...A146 - 158
1161(chain A and (resid 7 through 11 or resid 14...A160
211(chain B and (resid 7 through 11 or resid 14...B7 - 11
221(chain B and (resid 7 through 11 or resid 14...B14 - 32
231(chain B and (resid 7 through 11 or resid 14...B34 - 38
241(chain B and (resid 7 through 11 or resid 14...B5 - 52
251(chain B and (resid 7 through 11 or resid 14...B54 - 56
261(chain B and (resid 7 through 11 or resid 14...B60 - 67
271(chain B and (resid 7 through 11 or resid 14...B69 - 71
281(chain B and (resid 7 through 11 or resid 14...B73 - 90
291(chain B and (resid 7 through 11 or resid 14...B5 - 161
2101(chain B and (resid 7 through 11 or resid 14...B91 - 106
2111(chain B and (resid 7 through 11 or resid 14...B0
2121(chain B and (resid 7 through 11 or resid 14...B5 - 161
2131(chain B and (resid 7 through 11 or resid 14...B5 - 161
2141(chain B and (resid 7 through 11 or resid 14...B141 - 144
2151(chain B and (resid 7 through 11 or resid 14...B146 - 158
2161(chain B and (resid 7 through 11 or resid 14...B160

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Components

#1: Protein Beta-lactoglobulin / / Beta-LG


Mass: 18155.141 Da / Num. of mol.: 2 / Mutation: Q59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capra hircus (goat) / Gene: LGB / Plasmid: pETDuet-1 / Details (production host): DsbC (MSCI), cBLG-Ala59 (MSCII) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: P02756
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium sulfate, 0.1 M Bis-Tris (pH 6.5), 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.69→45.271 Å / Num. obs: 29406 / % possible obs: 98.8 % / Redundancy: 11 % / CC1/2: 0.992 / Rmerge(I) obs: 0.459 / Rpim(I) all: 0.135 / Rrim(I) all: 0.479 / Net I/σ(I): 4.2
Reflection shellResolution: 2.69→2.82 Å / Rmerge(I) obs: 1.403 / Num. unique obs: 1060 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tlj

4tlj


Resolution: 3→45.271 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 539 4.7 %
Rwork0.2367 10925 -
obs0.2387 11464 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.71 Å2 / Biso mean: 40.0986 Å2 / Biso min: 1.81 Å2
Refinement stepCycle: final / Resolution: 3→45.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 0 6 2467
Biso mean---27.44 -
Num. residues----313
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A676X-RAY DIFFRACTION5.452TORSIONAL
12B676X-RAY DIFFRACTION5.452TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.0002-3.3020.30431370.25892727
3.302-3.77960.32271530.25522727
3.7796-4.76110.25041300.21292721
4.7611-45.2710.23361190.23292750
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)
10.0010.0029-0.00030.00420.00070.0002-0.0091-0.00020.00070.0004-0.0049-0.00050.0016-0.0062-00.3718-0.00170.04460.3812-0.01490.3567-24.5866-6.0578-3.7841
20.01950.00380.01050.0176-0.01110.0119-0.07420.0239-0.0705-0.05660.0007-0.0452-0.0409-0.02760-0.2467-0.01070.13920.05590.04560.0143-15.0975-7.0104-15.3985
3-0.0007-0.00040.0008-0.00050.0003-0.0023-0.00720.00190.00450.0046-0-0.0025-0.0139-0.010900.2614-0.04460.08930.0910.00130.1971-5.24532.3732-21.5751
40.0018-0.0012-0.0048-0.00080.0008-0.00090.04950.0520.0045-0.04190.0298-0.0134-0.01410.0118-0-0.14680.07160.0086-0.13080.1363-0.0049-1.201217.0622-25.7474
5-0.0009-0.0021-0.0028-0.0005-0.00120.00220.00460.03420.0164-0.00350.0081-0.0013-0.00470.000700.14260.03380.10450.06260.05640.05446.438618.6891-29.0597
60.00820.0061-0.0040.0039-0.00070.0070.01970.00110.0128-0.0228-0.0096-0.0254-0.0248-0.0433-00.07440.08870.1363-0.15460.02610.0151-7.177123.5837-26.2688
7-0.0006-0.00110.002-0.00160.00470.00410.0059-0.04710.00730.00910.0128-0.02640.00320.0474-0-0.12870.0595-0.02320.05290.0156-0.0886-7.018115.337-16.1738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 11 )A4 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 160 )A12 - 160
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 19 )B5 - 19
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 53 )B20 - 53
5X-RAY DIFFRACTION5chain 'B' and (resid 54 through 73 )B54 - 73
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 129 )B74 - 129
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 161 )B130 - 161

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