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- PDB-7vgo: Hen egg lysozyme -

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Basic information

Entry
Database: PDB / ID: 7vgo
TitleHen egg lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme
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 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 bacterium / defense response to Gram-positive 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsOda, M. / Ikura, T. / Ito, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein J. / Year: 2022
Title: Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH.
Authors: Oda, M. / Sano, T. / Kamatari, Y.O. / Abe, Y. / Ikura, T. / Ito, N.
History
DepositionSep 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,5197
Polymers14,3311
Non-polymers1886
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-56 kcal/mol
Surface area6510 Å2
Unit cell
Length a, b, c (Å)78.816, 78.816, 36.917
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-327-

HOH

21A-360-

HOH

31A-409-

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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.1M sodium acetate, 8%(w/v) sodium chloride, 0.1M cesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 36189 / % possible obs: 97.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 11.5 Å2 / Rsym value: 0.049 / Net I/σ(I): 66.38
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 6.28 % / Mean I/σ(I) obs: 6.8 / Num. unique obs: 1522 / CC1/2: 0.941 / Rsym value: 0.383 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4QEQ

4qeq


Resolution: 1.2→25.49 Å / SU ML: 0.0749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.7556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1616 1818 5.03 %
Rwork0.1446 34316 -
obs0.1455 36134 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.34 Å2
Refinement stepCycle: LAST / Resolution: 1.2→25.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 6 113 1119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481035
X-RAY DIFFRACTIONf_angle_d0.87811403
X-RAY DIFFRACTIONf_chiral_restr0.0883146
X-RAY DIFFRACTIONf_plane_restr0.01185
X-RAY DIFFRACTIONf_dihedral_angle_d5.8537146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.16191160.14142273X-RAY DIFFRACTION85.23
1.23-1.270.16581200.13562517X-RAY DIFFRACTION94.65
1.27-1.310.16491620.12922604X-RAY DIFFRACTION99.5
1.31-1.360.15931500.1282640X-RAY DIFFRACTION100
1.36-1.410.14961440.11692664X-RAY DIFFRACTION99.96
1.41-1.480.14161380.11322674X-RAY DIFFRACTION99.96
1.48-1.550.14311320.11572679X-RAY DIFFRACTION100
1.55-1.650.13851310.11582679X-RAY DIFFRACTION100
1.65-1.780.15761430.12932701X-RAY DIFFRACTION100
1.78-1.960.14241550.1362682X-RAY DIFFRACTION99.93
1.96-2.240.15051330.13152733X-RAY DIFFRACTION100
2.24-2.820.16411510.1562756X-RAY DIFFRACTION99.97
2.82-25.490.18491430.17642714X-RAY DIFFRACTION93.46

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