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- PDB-1ix0: I59A-3SS human lysozyme -

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Basic information

Entry
Database: PDB / ID: 1ix0
TitleI59A-3SS human lysozyme
Componentslysozyme
KeywordsHYDROLASE / stability / water
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 / SYNCHROTRON / isomorphous / Resolution: 1.8 Å
AuthorsTakano, K. / Yamagata, Y. / Yutani, K.
Citation
Journal: PROTEIN ENG. / Year: 2003
Title: Buried water molecules contribute to the conformational stability of a protein
Authors: Takano, K. / Yamagata, Y. / Yutani, K.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: A general rule for the relationship between hydrophobic effect and conformational stability of a protein: stability and structure of a series of hydrophobic mutants of human lysozyme
Authors: Takano, K. / Yamagata, Y. / Yutani, K.
History
DepositionJun 6, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6372
Polymers14,6141
Non-polymers231
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.83, 60.88, 32.10
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein lysozyme / Lysozyme C


Mass: 14614.482 Da / Num. of mol.: 1 / Mutation: I59A/C77A/C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61626, lysozyme
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion, hanging drop / Details: Takano, K., (1995) J.Mol.Biol., 254, 62.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22.5 M1reservoirNaCl
320 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. all: 50796 / Num. obs: 10772 / % possible obs: 99 %
Reflection
*PLUS
Num. measured all: 50796 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 35

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: isomorphous / Resolution: 1.8→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.179 -
obs-10565
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 1 248 1273
Refinement
*PLUS
Rfactor Rfree: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.009
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.49

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