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

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Basic information

Entry
Database: PDB / ID: 8fsw
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
Water2,360131
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)77.357, 77.357, 37.164
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-332-

HOH

21A-425-

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.: 131 / 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: Jan 14, 2021
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→14.05 Å / Num. obs: 15248 / % possible obs: 99.1 % / Redundancy: 4.7 % / CC1/2: 0.93 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.141 / Rrim(I) all: 0.314 / Χ2: 0.71 / Net I/σ(I): 7.5 / Num. measured all: 72224
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 99.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 5.957 / Num. measured all: 2258 / Num. unique obs: 788 / CC1/2: 0.159 / Rpim(I) all: 3.971 / Rrim(I) all: 7.201 / Χ2: 0.62 / Net I/σ(I) obs: 0.6

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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→14.05 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.472 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26518 746 4.9 %RANDOM
Rwork0.22215 ---
obs0.22421 14471 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å2-0 Å2
2--0.35 Å20 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.6→14.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 1 131 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131024
X-RAY DIFFRACTIONr_bond_other_d0.0010.018904
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6321387
X-RAY DIFFRACTIONr_angle_other_deg1.4821.5872085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08820.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4911511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
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_it1.4181.631514
X-RAY DIFFRACTIONr_mcbond_other1.4171.631514
X-RAY DIFFRACTIONr_mcangle_it2.2612.449642
X-RAY DIFFRACTIONr_mcangle_other2.262.453643
X-RAY DIFFRACTIONr_scbond_it2.4161.918509
X-RAY DIFFRACTIONr_scbond_other2.4141.921510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6762.773746
X-RAY DIFFRACTIONr_long_range_B_refined5.20420.0011268
X-RAY DIFFRACTIONr_long_range_B_other4.95819.531240
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
Rfree0.394 66 -
Rwork0.429 1051 -
obs--99.47 %

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