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- PDB-4xyy: Hen Egg-White Lysozyme (HEWL) complexed with Zr(IV)-substituted K... -

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Basic information

Entry
Database: PDB / ID: 4xyy
TitleHen Egg-White Lysozyme (HEWL) complexed with Zr(IV)-substituted Keggin-type polyoxometalate
ComponentsLysozyme C
KeywordsHYDROLASE / Co-crystallization / lysozyme / metalsubstituted polyoxometalates
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
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
ETHANE-1,2-DIAMINE / ZIRCONIUM(IV) PHOSPHOTUNGSTATE KEGGIN / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsDe Zitter, E. / Van Meervelt, L.
CitationJournal: Chemistry / Year: 2015
Title: Structural Characterization of the Complex between Hen Egg-White Lysozyme and Zr(IV) -Substituted Keggin Polyoxometalate as Artificial Protease.
Authors: Sap, A. / De Zitter, E. / Van Meervelt, L. / Parac-Vogt, T.N.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Dec 12, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_nat / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.3Jan 10, 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)17,2995
Polymers14,3311
Non-polymers2,9684
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.232, 77.232, 37.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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-ZKG / ZIRCONIUM(IV) PHOSPHOTUNGSTATE KEGGIN


Mass: 2769.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: O39PW11Zr
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDN / ETHANE-1,2-DIAMINE / ETHYLENEDIAMINE / Ethylenediamine


Mass: 60.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.97 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1 M Sodium HEPES pH 7.5, 2.0 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.38→38.62 Å / Num. obs: 45045 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 15.41 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.2
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASER2.5.6phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.38→38.616 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 2245 4.99 %Random selection
Rwork0.1618 42784 --
obs0.1629 45029 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.33 Å2 / Biso mean: 21.2734 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 1.38→38.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 64 164 1229
Biso mean--22.59 31.33 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131190
X-RAY DIFFRACTIONf_angle_d2.041728
X-RAY DIFFRACTIONf_chiral_restr0.061157
X-RAY DIFFRACTIONf_plane_restr0.006202
X-RAY DIFFRACTIONf_dihedral_angle_d12.545472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.410.30521420.28042689283199
1.41-1.44280.25331390.250926392778100
1.4428-1.47890.24411400.21022670281099
1.4789-1.51890.24231380.18622655279399
1.5189-1.56360.18811400.178327022842100
1.5636-1.61410.17091420.15626432785100
1.6141-1.67170.19941400.157826702810100
1.6717-1.73870.22071400.164326712811100
1.7387-1.81780.19141410.15726752816100
1.8178-1.91360.18551410.157326992840100
1.9136-2.03350.19081400.151526642804100
2.0335-2.19050.21211410.154126772818100
2.1905-2.41090.14771400.155426882828100
2.4109-2.75970.17981370.162526842821100
2.7597-3.47660.16881430.1626762819100
3.4766-38.63110.16891410.151326822823100

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