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- PDB-7s34: Crystal structure of hen egg white lysozyme -

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Basic information

Entry
Database: PDB / ID: 7s34
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 / 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: 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 4, 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 13, 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
Water2,630146
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)77.238, 77.238, 37.112
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-323-

HOH

21A-355-

HOH

31A-420-

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.: 146 / 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: 1.93 Å3/Da / Density % sol: 36.31 % / Mosaicity: 1.07 °
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 12, 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→13.38 Å / Num. obs: 15294 / % possible obs: 99.6 % / Redundancy: 4.8 % / CC1/2: 0.935 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.1 / Num. measured all: 73015 / Scaling rejects: 459
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.6-1.6331.03122657620.0231.998.7
8.62-13.385.70.034464820.99927.969.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qwy

6qwy


Resolution: 1.6→13.38 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2331 / WRfactor Rwork: 0.2007 / FOM work R set: 0.8224 / SU B: 2.318 / SU ML: 0.08 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.1091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / 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
Rfree0.2381 751 4.9 %RANDOM
Rwork0.2002 ---
obs0.202 14512 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.66 Å2 / Biso mean: 15.843 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2--0.4 Å20 Å2
3----0.81 Å2
Refinement stepCycle: final / Resolution: 1.6→13.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 1 146 1147
Biso mean--21.55 27.74 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131024
X-RAY DIFFRACTIONr_bond_other_d0.0020.018904
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6321387
X-RAY DIFFRACTIONr_angle_other_deg1.5521.5872085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42920.65661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2031511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021179
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02246
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 65 -
Rwork0.246 1031 -
all-1096 -
obs--98.56 %

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