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- PDB-8z51: Hen Egg-White Lysozyme (HEWL) complexed with Emetine -

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Basic information

Entry
Database: PDB / ID: 8z51
TitleHen Egg-White Lysozyme (HEWL) complexed with Emetine
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
emetine / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 Emetine
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)14,8122
Polymers14,3311
Non-polymers4811
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.191, 79.191, 35.335
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-414-

HOH

21A-461-

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-34G / emetine / (3beta,14beta)-6',7',10,11-tetramethoxyemetan


Mass: 480.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.93 Å3/Da / Density % sol: 36.36 %
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: 1.5→21.96 Å / Num. obs: 18512 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 10.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.104 / Net I/σ(I): 17.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3447 / CC1/2: 0.709 / Rpim(I) all: 0.287 / Rrim(I) all: 0.731 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→21.96 Å / SU ML: 0.1515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 2671 7.78 %
Rwork0.175 31657 -
obs0.178 18512 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 35 172 1208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651097
X-RAY DIFFRACTIONf_angle_d1.25731494
X-RAY DIFFRACTIONf_chiral_restr0.1195155
X-RAY DIFFRACTIONf_plane_restr0.0076193
X-RAY DIFFRACTIONf_dihedral_angle_d11.8218174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.25621430.23871678X-RAY DIFFRACTION99.89
1.53-1.560.26811370.22931658X-RAY DIFFRACTION99.72
1.56-1.590.24241450.22541673X-RAY DIFFRACTION100
1.59-1.620.23711370.20331649X-RAY DIFFRACTION100
1.62-1.660.21581440.21191660X-RAY DIFFRACTION100
1.66-1.70.27751410.19781713X-RAY DIFFRACTION100
1.7-1.750.29981340.19571650X-RAY DIFFRACTION100
1.75-1.80.23971410.18911662X-RAY DIFFRACTION100
1.8-1.860.27041410.18341676X-RAY DIFFRACTION99.94
1.86-1.920.23221420.17571673X-RAY DIFFRACTION100
1.92-20.16341390.16931669X-RAY DIFFRACTION100
2-2.090.2081300.1661660X-RAY DIFFRACTION100
2.09-2.20.2181440.1711687X-RAY DIFFRACTION99.95
2.2-2.340.20941440.16181664X-RAY DIFFRACTION100
2.34-2.520.2071410.16181652X-RAY DIFFRACTION100
2.52-2.770.20111420.1751659X-RAY DIFFRACTION100
2.77-3.170.22631420.17291695X-RAY DIFFRACTION100
3.17-3.990.19061470.14691653X-RAY DIFFRACTION99.94
4-21.960.16981370.16321626X-RAY DIFFRACTION97.19

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