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- PDB-6hyb: Zr(IV)-substituted Wells-Dawson binding to Hen Egg-White Lysozyme... -

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Basic information

Entry
Database: PDB / ID: 6hyb
TitleZr(IV)-substituted Wells-Dawson binding to Hen Egg-White Lysozyme (HEWL)
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / co-crystal / polyoxometalate / catalysis
Function / homology
Function and homology information


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 ...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
Lysozyme - #10 / 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 / Lysozyme-like domain superfamily ...Lysozyme - #10 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / W-Zr-cluster / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.964 Å
AuthorsVandebroek, L. / Van Meervelt, L. / Parac-Vogt, T.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
CitationJournal: Eur J Inorg Chem / Year: 2019
Title: Noncovalent Complexes Formed between Metal-Substituted Polyoxometalates and Hen Egg White Lysozyme
Authors: Vandebroek, L. / Mampaey, Y. / Antonyuk, S. / Van Meervelt, L. / Parac-Vogt, T.N.
History
DepositionOct 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,5143
Polymers14,2181
Non-polymers4,2962
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.610, 78.610, 37.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

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Components

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


Mass: 14218.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-ZRW / W-Zr-cluster


Mass: 4256.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O61P2W17Zr / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4
Details: 1.75 mM HEWL, 0.8 mM 1:1 Zr(IV)-Wells-Dawson, 1 M LiCl, 30% PEG 6000, 0.1 M Citric acid pH = 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.96→35.16 Å / Num. obs: 15576 / % possible obs: 98.6 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.89
Reflection shellResolution: 1.96→2.08 Å / Rmerge(I) obs: 0.806

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1LYZ

1lyz


Resolution: 1.964→35.155 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.08 / Details: Phenix.refine v 1.12
RfactorNum. reflection% reflection
Rfree0.2045 781 5.01 %
Rwork0.171 --
obs0.1728 15576 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.03 Å2 / Biso mean: 39.0864 Å2 / Biso min: 0.01 Å2
Refinement stepCycle: final / Resolution: 1.964→35.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 95 58 1130
Biso mean--26.37 39.13 -
Num. residues----128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9641-2.08720.31461210.26732242236390
2.0872-2.24830.29751310.21225172648100
2.2483-2.47450.20821310.166425282659100
2.4745-2.83250.21621280.162424982626100
2.8325-3.56810.22321320.162925062638100
3.5681-35.16110.15981380.160325042642100

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