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- PDB-7s28: Crystal structure of hen egg white lysozyme -

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Basic information

Entry
Database: PDB / ID: 7s28
TitleCrystal structure of hen egg white lysozyme
ComponentsLysozyme C
KeywordsHYDROLASE
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsLima, L.M.T.R. / Ramos, N.G. / Ribeiro, F.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Anal.Biochem. / Year: 2022
Title: The reproducible normality of the crystallographic B-factor.
Authors: Ramos, N.G. / Sarmanho, G.F. / de Sa Ribeiro, F. / de Souza, V. / Lima, L.M.T.R.
History
DepositionSep 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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)14,3542
Polymers14,3311
Non-polymers231
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.495, 78.495, 36.980
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-382-

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 / Details: egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 4.6
Details: 1.2 M NaCl, 100 mM Sodium Acetate, 50 mg/mL Lyzozyme, 30% Glycerol for cryoprotection

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.54184 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Dec 12, 2020
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.6→22.21 Å / Num. obs: 15818 / % possible obs: 99.89 % / Redundancy: 9.04 % / Rsym value: 0.074 / Net I/av σ(I): 11.02 / Net I/σ(I): 11.02
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
1.6-1.657271270.2571
1.657-1.723241730.211
1.723-1.802211610.1641
1.802-1.897182020.1271
1.897-2.015151720.1051
2.015-2.171121760.0911
2.171-2.38991800.0861
2.389-2.73461660.0751
2.734-3.44331180.0631
3.443-22.21291780.0531

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SAINTV8.40Adata scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qwy

6qwy


Resolution: 1.6→22.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1946 / WRfactor Rwork: 0.1688 / FOM work R set: 0.8833 / SU B: 1.437 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0955 / SU Rfree: 0.0912 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: isomorphous replacement with REFMAC , restrained refinement with REFMAC, real space refinement with C.O.O.T.
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 802 5.1 %RANDOM
Rwork0.1752 ---
obs0.1766 14974 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.02 Å2 / Biso mean: 11.111 Å2 / Biso min: 0.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0 Å2
2--0.13 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.6→22.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 1 157 1158
Biso mean--7.98 22.68 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131024
X-RAY DIFFRACTIONr_bond_other_d0.0010.018904
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.6321387
X-RAY DIFFRACTIONr_angle_other_deg1.6651.5872085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89920.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3921511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.173 62 -
Rwork0.16 1060 -
obs--99.56 %

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