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- PDB-5fhw: Hen Egg-White Lysozyme (HEWL) complexed with Hf(IV)-substituted W... -

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Basic information

Entry
Database: PDB / ID: 5fhw
TitleHen Egg-White Lysozyme (HEWL) complexed with Hf(IV)-substituted Wells Dawson-type polyoxometalate
ComponentsLysozyme C
KeywordsHYDROLASE / Complex / polyoxometalate / hafnium / Wells Dawson
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
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
Dawson-type polyoxometalate / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 Å
AuthorsVandebroek, L. / De Zitter, E. / Van Meervelt, L.
CitationJournal: To Be Published
Title: Structural Characterization of the Complex between Hen Egg- White Lysozyme and HfIV-Substituted Wells Dawson Polyoxometalate as Artificial Protease
Authors: Vandebroek, L. / De Zitter, E. / Van Meervelt, L. / Parac-Vogt, T.N.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / pdbx_entity_src_syn / pdbx_struct_special_symmetry
Item: _entity.src_method
Revision 1.2Jan 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)18,7534
Polymers14,3311
Non-polymers4,4223
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.951, 78.951, 36.756
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-201-

HFW

21A-379-

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-HFW / Dawson-type polyoxometalate


Mass: 4343.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HfO61P2W17
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25 mg/mL Lysozyme C, 1.45 mM 1:2 Hf-Wells Dawson, 2.0 M sodium chloride, 0.1 M potassium phosphate monobasic, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M MES pH = 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→39.48 Å / Num. all: 130169 / Num. obs: 18463 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.048 / Net I/σ(I): 17.3 / Num. measured all: 130169
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.52-1.557.30.5993.364048830.9270.237100
8.33-39.485.60.05161.78491520.9980.02199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.52 Å35.31 Å
Translation1.52 Å35.31 Å

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.6.0phasing
PHENIX1.1refinement
PDB_EXTRACT3.15data extraction
XDS13.4.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VB1

2vb1


Resolution: 1.52→35.308 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 889 4.84 %
Rwork0.1603 17497 -
obs0.1617 18386 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.97 Å2 / Biso mean: 19.2414 Å2 / Biso min: 9.1 Å2
Refinement stepCycle: final / Resolution: 1.52→35.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 83 172 1256
Biso mean--13.78 26.61 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111155
X-RAY DIFFRACTIONf_angle_d1.9691750
X-RAY DIFFRACTIONf_chiral_restr0.068154
X-RAY DIFFRACTIONf_plane_restr0.006186
X-RAY DIFFRACTIONf_dihedral_angle_d16.249719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.52-1.61530.2291430.187828562999100
1.6153-1.740.17851220.16782870299299
1.74-1.91510.1931170.162928903007100
1.9151-2.19210.21081580.161129003058100
2.1921-2.76170.18661720.169829033075100
2.7617-35.31750.17641770.147830783255100

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