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- PDB-8fsv: Crystal structure of hen egg white lysozyme -

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Basic information

Entry
Database: PDB / ID: 8fsv
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 / 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: 1.6 Å
AuthorsLima, L.M.T.R. / Ramos, N.G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: To Be Published
Title: Crystal structure of hen egg white lysozyme
Authors: Lima, L.M.T.R. / Ramos, N.G.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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)14,3542
Polymers14,3311
Non-polymers231
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.160, 77.160, 37.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

21A-349-

HOH

31A-417-

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: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.99 Å3/Da / Density % sol: 38.22 %
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: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å
DetectorType: OXFORD TITAN CCD / Detector: CCD / Date: Dec 15, 2020
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.6→13.37 Å / Num. obs: 15309 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Χ2: 0.68 / Net I/σ(I): 10 / Num. measured all: 69982
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 98 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.443 / Num. measured all: 2137 / Num. unique obs: 754 / CC1/2: 0.774 / Rpim(I) all: 0.305 / Rrim(I) all: 0.541 / Χ2: 0.42 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→13.37 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 2.681 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24996 752 4.9 %RANDOM
Rwork0.20539 ---
obs0.20753 14523 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0 Å2
2--0.44 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.6→13.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 1 142 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131024
X-RAY DIFFRACTIONr_bond_other_d0.0010.018904
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6321387
X-RAY DIFFRACTIONr_angle_other_deg1.4971.5872085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39520.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2521511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021179
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02246
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1991.45514
X-RAY DIFFRACTIONr_mcbond_other1.1991.45514
X-RAY DIFFRACTIONr_mcangle_it1.9282.175642
X-RAY DIFFRACTIONr_mcangle_other1.9262.179643
X-RAY DIFFRACTIONr_scbond_it1.9861.726509
X-RAY DIFFRACTIONr_scbond_other1.9841.729510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1392.49746
X-RAY DIFFRACTIONr_long_range_B_refined4.85818.5931285
X-RAY DIFFRACTIONr_long_range_B_other4.74418.1861260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 64 -
Rwork0.257 1020 -
obs--98.28 %

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