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- PDB-3ww6: Crystal Structure of hen egg white lysozyme mutant N46D/D52S -

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Basic information

Entry
Database: PDB / ID: 3ww6
TitleCrystal Structure of hen egg white lysozyme mutant N46D/D52S
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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsAbe, Y. / Kubota, M. / Ito, Y. / Imoto, T. / Ueda, T.
CitationJournal: Protein Sci. / Year: 2016
Title: Effect on catalysis by replacement of catalytic residue from hen egg white lysozyme to Venerupis philippinarum lysozyme.
Authors: Abe, Y. / Kubota, M. / Takazaki, S. / Ito, Y. / Yamamoto, H. / Kang, D. / Ueda, T. / Imoto, T.
History
DepositionJun 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,4816
Polymers14,3041
Non-polymers1775
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.006, 77.006, 37.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14304.135 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Mutation: N46D, D52S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Plasmid: pPICZ-alfa / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 36.17 % / Mosaicity: 0.751 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.6M sodium chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2012
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 17242 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Χ2: 5.923 / Net I/σ(I): 76.659
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.53-1.5812.90.21116923.599199.9
1.58-1.6513.10.17117134.156199.9
1.65-1.7213.20.14817014.6051100
1.72-1.8113.30.12617174.9831100
1.81-1.9313.40.11117146.0861100
1.93-2.0813.40.09817297.09199.8
2.08-2.2913.60.08517297.059199.8
2.29-2.6213.60.07817557.177199.7
2.62-3.313.20.07217548.143198.4
3.3-5011.80.05517386.057191.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å26.75 Å
Translation3 Å26.75 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2lzt

2lzt


Resolution: 1.53→26.748 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8646 / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 871 5.07 %RANDOM
Rwork0.1869 ---
obs0.1878 17190 98.55 %-
all-17190 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.41 Å2 / Biso mean: 15.4076 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: LAST / Resolution: 1.53→26.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 5 112 1116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061035
X-RAY DIFFRACTIONf_angle_d1.0951395
X-RAY DIFFRACTIONf_chiral_restr0.085145
X-RAY DIFFRACTIONf_plane_restr0.003183
X-RAY DIFFRACTIONf_dihedral_angle_d11.7371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5294-1.62520.22091440.17122666281098
1.6252-1.75070.22461560.171726872843100
1.7507-1.92680.24851550.177426992854100
1.9268-2.20550.20081590.179227302889100
2.2055-2.77820.19691330.196127632896100
2.7782-26.75170.19321240.19142774289894

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