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- PDB-7wql: Bovin Beta-lactoglobulin binding with zinc ions -

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Basic information

Entry
Database: PDB / ID: 7wql
TitleBovin Beta-lactoglobulin binding with zinc ions
ComponentsBeta-lactoglobulin
KeywordsMETAL BINDING 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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsLi, T. / Ma, J. / Zang, J. / Zhao, G. / Zhang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31901638 China
CitationJournal: Rsc Adv / Year: 2022
Title: Zinc binding strength of proteins dominants zinc uptake in Caco-2 cells.
Authors: Li, T. / Jiao, R. / Ma, J. / Zang, J. / Zhao, G. / Zhang, T.
History
DepositionJan 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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
A: Beta-lactoglobulin
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9958
Polymers36,6022
Non-polymers3926
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-133 kcal/mol
Surface area15060 Å2
Unit cell
Length a, b, c (Å)132.148, 42.464, 70.037
Angle α, β, γ (deg.)90.000, 104.050, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18301.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 200 mM Ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 25390 / % possible obs: 98.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Χ2: 0.659 / Net I/σ(I): 5 / Num. measured all: 84557
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.10.43412270.8690.2810.5190.4596.8
2.03-2.073.20.42612420.8640.2750.5090.47398.9
2.07-2.113.30.34112750.9110.2190.4070.47498.2
2.11-2.153.10.33712550.9180.2210.4040.55299
2.15-2.23.10.3212370.9040.2110.3850.63997.6
2.2-2.253.50.26412810.9320.1640.3120.65898.7
2.25-2.313.50.23112590.9520.1430.2730.64699.5
2.31-2.373.50.19312590.970.120.2270.52699.2
2.37-2.443.40.18112660.9760.1130.2140.54499.3
2.44-2.523.40.15312800.9750.0960.1820.55798.4
2.52-2.613.20.13512480.980.0880.1620.55597.3
2.61-2.713.20.11812460.9820.0770.1410.6197.9
2.71-2.843.50.10412930.9880.0640.1220.64399.2
2.84-2.993.50.08512720.9920.0530.10.65799.3
2.99-3.173.40.07512880.9930.0470.0890.74299.2
3.17-3.423.30.06112440.9940.0390.0730.81996.6
3.42-3.763.40.05212930.9950.0330.0620.85499.5
3.76-4.313.50.04613070.9960.0290.0540.87199.7
4.31-5.423.30.03812900.9980.0250.0450.85797.6
5.42-103.30.03713280.9980.0240.0440.96298.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IO5

5io5


Resolution: 2.001→33.971 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1997 7.87 %
Rwork0.2071 23375 -
obs0.2113 25372 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.94 Å2 / Biso mean: 44.99 Å2 / Biso min: 17.37 Å2
Refinement stepCycle: final / Resolution: 2.001→33.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 6 114 2601
Biso mean--57.05 41.75 -
Num. residues----314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.001-2.05070.31531380.258160997
2.0507-2.10610.29131410.2449167198
2.1061-2.16810.30971380.246163499
2.1681-2.23810.27661440.2297167398
2.2381-2.31810.25751400.2151164999
2.3181-2.41080.28351450.2136168499
2.4108-2.52050.29921410.2269165398
2.5205-2.65340.27231420.2136165497
2.6534-2.81950.31321440.21421689100
2.8195-3.03710.30031430.2257167899
3.0371-3.34250.28161420.2206165498
3.3425-3.82560.27951440.1956168899
3.8256-4.81770.20561470.1667171499
4.8177-100.22681480.2076172597

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