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- PDB-1flq: HEN EGG WHITE LYSOZYME MUTANT WITH ALANINE SUBSTITUTED FOR GLYCINE -

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Basic information

Entry
Database: PDB / ID: 1flq
TitleHEN EGG WHITE LYSOZYME MUTANT WITH ALANINE SUBSTITUTED FOR GLYCINE
ComponentsLYSOZYME
KeywordsHYDROLASE / HEN LYSOZYME / ALANINE SCANNING
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 / Resolution: 1.801 Å
AuthorsMasumoto, K. / Ueda, T. / Motoshima, H. / Imoto, T.
CitationJournal: Protein Eng. / Year: 2000
Title: Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine
Authors: Masumoto, K. / Ueda, T. / Motoshima, H. / Imoto, T.
History
DepositionAug 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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


Theoretical massNumber of molelcules
Total (without water)14,3451
Polymers14,3451
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.24, 79.24, 37.86
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein LYSOZYME / E.C.3.2.1.17 / 1 / 4-BETA-N-ACETYLMURAMIDASE C / ALLERGEN GAL D 4 / GAL D IV


Mass: 14345.186 Da / Num. of mol.: 1 / Mutation: G117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PAM82 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: sodium chloride, sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
PH range low: 3.2 / PH range high: 2.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 Mglycine1drop
20.7-1.5 mg/mlprotein1drop
350 mMsodium acetate1reservoir
40.6-0.9 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.801→6 Å / Num. all: 11664 / Num. obs: 10589 / Redundancy: 1.1 % / Rmerge(I) obs: 0.0519
Reflection
*PLUS
% possible obs: 90.8 % / Num. measured all: 11664

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 1.801→6 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1057 10 %RANDOM
Rwork0.164 ---
all0.169 11664 --
obs-10589 --
Refinement stepCycle: LAST / Resolution: 1.801→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 67 1068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.492
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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