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- PDB-8bqp: Hen Egg-White Lysozyme (HEWL) complexed with methyl-functionalise... -

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Basic information

Entry
Database: PDB / ID: 8bqp
TitleHen Egg-White Lysozyme (HEWL) complexed with methyl-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 / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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
ACETATE ION / Mn-Mo(6)-O(24)-C(10) cluster / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)15,6145
Polymers14,3311
Non-polymers1,2834
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.388, 76.388, 36.981
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-348-

HOH

21A-389-

HOH

31A-408-

HOH

41A-444-

HOH

51A-453-

HOH

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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-U7U / Mn-Mo(6)-O(24)-C(10) cluster / methyl-functionalised Anderson-Evans polyoxometalate


Mass: 1152.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18MnMo6O24 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 34.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 130 mg/mL Lysozyme, 20 mM AE-CH3, 1.0 M lithium chloride, 0.1 M sodium acetate and 30% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976253 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 1.24→38.19 Å / Num. obs: 31633 / % possible obs: 100 % / Redundancy: 24.3 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.012 / Rrim(I) all: 0.061 / Χ2: 1.02 / Net I/σ(I): 28.4 / Num. measured all: 768146
Reflection shellResolution: 1.24→1.26 Å / % possible obs: 100 % / Redundancy: 24 % / Rmerge(I) obs: 0.781 / Num. measured all: 36443 / Num. unique obs: 1519 / CC1/2: 0.931 / Rpim(I) all: 0.161 / Rrim(I) all: 0.798 / Χ2: 1.08 / Net I/σ(I) obs: 4.7

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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: 1.24→38.19 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1671 2973 5.02 %
Rwork0.1441 --
obs0.1453 31633 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 47 154 1199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.018
X-RAY DIFFRACTIONf_dihedral_angle_d6.746151
X-RAY DIFFRACTIONf_chiral_restr0.085148
X-RAY DIFFRACTIONf_plane_restr0.027190
LS refinement shellResolution: 1.24→1.26 Å
RfactorNum. reflection% reflection
Rfree0.2156 145 -
Rwork0.1827 2650 -
obs--100 %

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