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- PDB-6hy6: Ni(II)-substituted Wells-Dawson binding to Hen Egg-White Lysozyme... -

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Basic information

Entry
Database: PDB / ID: 6hy6
TitleNi(II)-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
Ni(II)-substituted Wells-Dawson / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 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
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4773
Polymers14,2181
Non-polymers4,2592
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.937, 78.937, 37.272
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
11B-201-

GXZ

21B-201-

GXZ

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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-GXZ / Ni(II)-substituted Wells-Dawson


Mass: 4223.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2NiO61P2W17
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.04 Å3/Da / Density % sol: 39.76 % / Mosaicity: 0.31 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 4
Details: 1.40 mM HEWL, 1.0 mM 1:1 Ni(II)-Wells-Dawson, 0.75 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: 1.87→39.47 Å / Num. obs: 10230 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 22.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.039 / Rrim(I) all: 0.149 / Net I/σ(I): 20.5 / Num. measured all: 144540 / Scaling rejects: 770
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.87-1.9114.90.78795296380.9630.2090.8146.1100
8.97-39.4710.10.06512581250.9980.020.06836.398.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.69 Å39.47 Å
Translation4.69 Å39.47 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.8.0phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LYZ

1lyz


Resolution: 1.87→33.704 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 18.86 / Stereochemistry target values: ML / Details: Phenix.refine v 1.12
RfactorNum. reflection% reflection
Rfree0.1919 888 4.77 %
Rwork0.1623 17709 -
obs0.1637 10200 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.45 Å2 / Biso mean: 26.916 Å2 / Biso min: 0.15 Å2
Refinement stepCycle: final / Resolution: 1.87→33.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 95 70 1140
Biso mean--14.39 31.36 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121126
X-RAY DIFFRACTIONf_angle_d1.1881716
X-RAY DIFFRACTIONf_chiral_restr0.062151
X-RAY DIFFRACTIONf_plane_restr0.015179
X-RAY DIFFRACTIONf_dihedral_angle_d17.427698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8702-1.98740.22341740.172329313105
1.9874-2.14080.21831390.159929713110
2.1408-2.35620.21241540.154329523106
2.3562-2.6970.22381340.151429443078
2.697-3.39740.1651350.164329563091
3.3974-33.70920.17751520.166429553107

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