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- PDB-1iy3: Solution Structure of the Human lysozyme at 4 degree C -

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Basic information

Entry
Database: PDB / ID: 1iy3
TitleSolution Structure of the Human lysozyme at 4 degree C
ComponentsLysozyme
KeywordsHYDROLASE / human lysozyme
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model type detailsminimized average
AuthorsKumeta, H. / Miura, A. / Kobashigawa, Y. / Miura, K. / Oka, C. / Nitta, K. / Nemoto, N. / Tsuda, S.
CitationJournal: Biochemistry / Year: 2003
Title: Low-temperature-induced structural changes in human lysozyme elucidated by three-dimensional NMR spectroscopy
Authors: Kumeta, H. / Miura, A. / Kobashigawa, Y. / Miura, K. / Oka, C. / Nemoto, N. / Nitta, K. / Tsuda, S.
History
DepositionJul 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 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


Theoretical massNumber of molelcules
Total (without water)14,7211
Polymers14,7211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Lysozyme / / Lysozyme C


Mass: 14720.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P61626, 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
1213D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 2mM Human lysozyme U-15N, 13C; 2.5M KCL, pH 3.8 adjusted at room temperature
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 2.5M KCL / pH: 3.8 / Pressure: ambient / Temperature: 277 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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe4.3.2Garrettdata analysis
X-PLOR3.8Brungerstructure solution
X-PLOR3.8Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 1

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