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- PDB-8d8e: Crystal structure of hen egg white lysozyme at 300 Kelvin (Triplicate) -

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Basic information

Entry
Database: PDB / ID: 8d8e
TitleCrystal structure of hen egg white lysozyme at 300 Kelvin (Triplicate)
ComponentsLysozyme C
KeywordsHYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRibeiro, F.S. / Lima, L.M.T.R.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Other government1 Brazil
Other government2 Brazil
CitationJournal: Biophys.Chem. / Year: 2023
Title: Linking B-factor and temperature-induced conformational transition.
Authors: de Sa Ribeiro, F. / Lima, L.M.T.R.
History
DepositionJun 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,78711
Polymers14,3311
Non-polymers45510
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.495, 79.495, 37.767
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-308-

HOH

21A-326-

HOH

31A-342-

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 genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1.2 M NaCl and 100 mM AcONa pH 4.6

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54184 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Nov 24, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.5→56.21 Å / Num. obs: 20015 / % possible obs: 99.58 % / Redundancy: 1.9 % / CC1/2: 0.806 / Net I/σ(I): 8.77
Reflection shellResolution: 1.5→56.21 Å / Num. unique obs: 18983 / CC1/2: 0.806

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A8Z

3a8z


Resolution: 1.5→56.21 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.48 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1959 1032 5.156 %
Rwork0.1746 18983 -
all0.176 --
obs-20015 99.582 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.015 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å2-0 Å2-0 Å2
2--0.001 Å2-0 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.5→56.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 20 42 1063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121035
X-RAY DIFFRACTIONr_bond_other_d0.0010.018950
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.6341399
X-RAY DIFFRACTIONr_angle_other_deg1.6151.5952164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04620.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9361511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
X-RAY DIFFRACTIONr_nbd_refined0.2350.2217
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.2881
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2529
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.228
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.020.22
X-RAY DIFFRACTIONr_nbd_other0.1170.215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.28
X-RAY DIFFRACTIONr_mcbond_it1.9711.891515
X-RAY DIFFRACTIONr_mcbond_other1.9381.885514
X-RAY DIFFRACTIONr_mcangle_it2.9122.835642
X-RAY DIFFRACTIONr_mcangle_other2.9122.841643
X-RAY DIFFRACTIONr_scbond_it3.9232.526520
X-RAY DIFFRACTIONr_scbond_other3.9192.536521
X-RAY DIFFRACTIONr_scangle_it6.0773.543757
X-RAY DIFFRACTIONr_scangle_other6.0733.554758
X-RAY DIFFRACTIONr_lrange_it7.48523.4381207
X-RAY DIFFRACTIONr_lrange_other7.48423.4861207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5350.394640.3371297X-RAY DIFFRACTION94.7112
1.535-1.5770.29650.3261358X-RAY DIFFRACTION99.9298
1.577-1.6220.321770.2851312X-RAY DIFFRACTION99.9281
1.622-1.6720.243540.2271273X-RAY DIFFRACTION99.9247
1.672-1.7270.23810.2141250X-RAY DIFFRACTION100
1.727-1.7880.196750.2011168X-RAY DIFFRACTION100
1.788-1.8550.22670.1841163X-RAY DIFFRACTION100
1.855-1.9310.285630.1731116X-RAY DIFFRACTION100
1.931-2.0170.173550.171070X-RAY DIFFRACTION100
2.017-2.1150.175560.1621034X-RAY DIFFRACTION100
2.115-2.2290.223580.158974X-RAY DIFFRACTION99.9032
2.229-2.3640.17520.152936X-RAY DIFFRACTION99.8989
2.364-2.5270.14420.167885X-RAY DIFFRACTION100
2.527-2.7290.197560.165815X-RAY DIFFRACTION100
2.729-2.9890.218400.178758X-RAY DIFFRACTION100
2.989-3.340.162310.166709X-RAY DIFFRACTION100
3.34-3.8550.206350.149624X-RAY DIFFRACTION100
3.855-4.7160.135340.133535X-RAY DIFFRACTION99.8246
4.716-6.6450.16200.163432X-RAY DIFFRACTION100
6.645-56.210.39370.177274X-RAY DIFFRACTION99.2933

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