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- PDB-1lyy: AMYLOIDOGENIC VARIANT (ASP67HIS) OF HUMAN LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1lyy
TitleAMYLOIDOGENIC VARIANT (ASP67HIS) OF HUMAN LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE / ENZYME / BETA-1 / 4-GLYCAN-HYDROLASE
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / lysozyme / lysozyme activity / tertiary granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSunde, M. / Blake, C.C.F.
CitationJournal: Nature / Year: 1997
Title: Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis.
Authors: Booth, D.R. / Sunde, M. / Bellotti, V. / Robinson, C.V. / Hutchinson, W.L. / Fraser, P.E. / Hawkins, P.N. / Dobson, C.M. / Radford, S.E. / Blake, C.C. / Pepys, M.B.
History
DepositionJan 16, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)14,7441
Polymers14,7441
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.340, 31.860, 51.500
Angle α, β, γ (deg.)90.00, 102.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LYSOZYME


Mass: 14743.752 Da / Num. of mol.: 1 / Mutation: D67H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HUMAN LYSOZYME CDNA AMPLIFIED FROM RNA / Plasmid: PBACPAK8 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P61626, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.04 Å3/Da / Density % sol: 40 %
Crystal growpH: 4
Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M AMMONIUM SULFATE, 30% PEG 8000, pH 4.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / PH range low: 8 / PH range high: 7.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMHEPES1drop
30.4-0.5 M1dropLiCl
40.16 Mammonium sulfate1reservoir
524 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 11071 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.103 / Rsym value: 0.131 / Net I/σ(I): 8.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3 / Rsym value: 0.223 / % possible all: 78.3
Reflection
*PLUS
Num. measured all: 41333
Reflection shell
*PLUS
% possible obs: 78.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN LYSOZYME COORDINATES FROM ARTYMUIK, P.J.AND BLAKE, C.C.F. J.MOL.BIOL. (1983) 167,693-723.

Resolution: 1.8→8 Å / Isotropic thermal model: RESTRAINED
Cross valid method: NOT USED AFTER INITIAL STAGES BECAUSE OF LOW NUMBER OF REFLECTIONS
σ(F): 0
RfactorNum. reflection% reflection
Rwork0.228 --
obs0.228 10216 92.2 %
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 0 115 1146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.98
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOP19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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