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- PDB-8bqr: Hen Egg-White Lysozyme (HEWL) complexed with biotin-functionalise... -

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Basic information

Entry
Database: PDB / ID: 8bqr
TitleHen Egg-White Lysozyme (HEWL) complexed with biotin-functionalised Anderson-Evans polyoxometalate
ComponentsLysozyme C
KeywordsHYDROLASE / interactions / polyoxometalate / Anderson-Evans
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-R9H / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLentink, S. / Salazar Marcano, D.E. / Moussawi, M.A. / Vandebroek, L. / Van Meervelt, L. / Parac-Vogt, T.N.
Funding support Belgium, 5items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1183021N Belgium
Research Foundation - Flanders (FWO)1279721N Belgium
Research Foundation - Flanders (FWO)11A3517N Belgium
Research Foundation - Flanders (FWO)G0E4717N Belgium
KU LeuvenC14/19/076 Belgium
CitationJournal: Faraday Disc.Chem.Soc / Year: 2023
Title: Fine-tuning non-covalent interactions between hybrid metal-oxo clusters and proteins.
Authors: Lentink, S. / Salazar Marcano, D.E. / Moussawi, M.A. / Vandebroek, L. / Van Meervelt, L. / Parac-Vogt, T.N.
History
DepositionNov 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9773
Polymers14,3311
Non-polymers1,6452
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.394, 79.394, 35.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-201-

R9H

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-R9H / Anderson-Evans polyoxometalate (biotin-functionalised)


Mass: 1605.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H42MnMo6N6O28S2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mg/mL Lysozyme, 200 mg/mL AE-Biot, of 0.5 M calcium chloride, 30% (w/v) PEG 4000 and 0.1 M HEPES buffer (pH 8.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.32→79.39 Å / Num. obs: 5101 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.019 / Rrim(I) all: 0.089 / Χ2: 0.89 / Net I/σ(I): 21.4
Reflection shellResolution: 2.34→2.42 Å / % possible obs: 99.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.684 / Num. measured all: 4136 / Num. unique obs: 467 / CC1/2: 0.878 / Rpim(I) all: 0.232 / Rrim(I) all: 0.724 / Χ2: 0.66 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless7.0.078data scaling
XDSVERSION Jan 10, 2022data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LYZ

1lyz


Resolution: 2.32→39.7 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2778 410 4.43 %
Rwork0.2512 --
obs0.2524 5101 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 72 15 1088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d2.711
X-RAY DIFFRACTIONf_dihedral_angle_d22.361
X-RAY DIFFRACTIONf_chiral_restr0.076
X-RAY DIFFRACTIONf_plane_restr0.019
LS refinement shellResolution: 2.32→2.4 Å
RfactorNum. reflection% reflection
Rfree0.3968 124 -
Rwork0.2993 2950 -
obs--99 %

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