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- PDB-8z52: Hen Egg-White Lysozyme (HEWL) complexed with Theophylline -

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Basic information

Entry
Database: PDB / ID: 8z52
TitleHen Egg-White Lysozyme (HEWL) complexed with Theophylline
ComponentsLysozyme C
KeywordsHYDROLASE / Lysozyme / Emetine / dimerization / drug-carrier
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
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
THEOPHYLLINE / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsRoy, A. / Khanppnavar, B. / Dolui, S. / Datta, S. / Maiti, N.C.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)GAP299 India
CitationJournal: To Be Published
Title: Hen Egg-White Lysozyme (HEWL) complexed with Theophylline
Authors: Roy, A. / Khanppnavar, B. / Dolui, S. / Datta, S. / Maiti, N.C.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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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)14,5112
Polymers14,3311
Non-polymers1801
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.378, 78.378, 36.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-364-

HOH

31A-510-

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-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Na-acetate pH 4.5, 6.5% (w/v) NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.48→22.159 Å / Num. obs: 19519 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Net I/σ(I): 11.5
Reflection shellResolution: 1.48→1.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3246 / CC1/2: 0.183 / Rpim(I) all: 0.44 / Rrim(I) all: 0.929 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→21.74 Å / SU ML: 0.1416 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 1952 10 %
Rwork0.1785 17567 -
obs0.1815 19519 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.92 Å2
Refinement stepCycle: LAST / Resolution: 1.48→21.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 13 215 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351084
X-RAY DIFFRACTIONf_angle_d0.69021476
X-RAY DIFFRACTIONf_chiral_restr0.0785151
X-RAY DIFFRACTIONf_plane_restr0.0043195
X-RAY DIFFRACTIONf_dihedral_angle_d23.0014401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.32461340.32011210X-RAY DIFFRACTION98.75
1.52-1.560.29491380.26291232X-RAY DIFFRACTION100
1.56-1.610.281380.23281241X-RAY DIFFRACTION100
1.61-1.660.26041370.21051228X-RAY DIFFRACTION100
1.66-1.720.24291350.19791220X-RAY DIFFRACTION100
1.72-1.790.26751380.19321246X-RAY DIFFRACTION100
1.79-1.870.22221380.1941236X-RAY DIFFRACTION100
1.87-1.970.20591390.17351257X-RAY DIFFRACTION100
1.97-2.090.19041380.171240X-RAY DIFFRACTION100
2.09-2.250.22221390.1581252X-RAY DIFFRACTION100
2.25-2.480.18281410.16281267X-RAY DIFFRACTION100
2.48-2.840.18021420.16321283X-RAY DIFFRACTION100
2.84-3.570.1651430.15711289X-RAY DIFFRACTION100
3.57-21.740.20071520.16251366X-RAY DIFFRACTION99.61

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