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- PDB-1ivm: Solution structure of mouse lysozyme M -

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Basic information

Entry
Database: PDB / ID: 1ivm
TitleSolution structure of mouse lysozyme M
Componentslysozyme M
KeywordsHYDROLASE / Glycosidase
Function / homology
Function and homology information


Antimicrobial peptides / Golgi cis cisterna / rough endoplasmic reticulum lumen / cytolysis / Golgi stack / trans-Golgi network transport vesicle / hydrolase activity, acting on glycosyl bonds / microvillus / metabolic process / Neutrophil degranulation ...Antimicrobial peptides / Golgi cis cisterna / rough endoplasmic reticulum lumen / cytolysis / Golgi stack / trans-Golgi network transport vesicle / hydrolase activity, acting on glycosyl bonds / microvillus / metabolic process / Neutrophil degranulation / secretory granule / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum lumen / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme C / 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 C / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsUeda, T. / Obita, T. / Imoto, T.
CitationJournal: CELL.MOL.LIFE SCI. / Year: 2003
Title: Solution structure and activity of mouse lysozyme M
Authors: Obita, T. / Ueda, T. / Imoto, T.
History
DepositionMar 27, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lysozyme M


Theoretical massNumber of molelcules
Total (without water)14,8401
Polymers14,8401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
RepresentativeModel #20fewest violations

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Components

#1: Protein lysozyme M / Lysozyme C / type M


Mass: 14839.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21d(+) / Production host: Pichia pastoris (fungus) / References: UniProt: P08905, lysozyme

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY

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Sample preparation

DetailsContents: 1mM mouse lysozyme U-15N; non-buffer / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3.8 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, P.structure solution
DYANA1.5Guentert, P.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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