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- PDB-1lz1: REFINEMENT OF HUMAN LYSOZYME AT 1.5 ANGSTROMS RESOLUTION. ANALYSI... -

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Basic information

Entry
Database: PDB / ID: 1lz1
TitleREFINEMENT OF HUMAN LYSOZYME AT 1.5 ANGSTROMS RESOLUTION. ANALYSIS OF NON-BONDED AND HYDROGEN-BOND INTERACTIONS
ComponentsHUMAN LYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / 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 / tertiary granule lumen / 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 / 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 / Resolution: 1.5 Å
AuthorsArtymiuk, P.J. / Blake, C.C.F.
Citation
Journal: J.Mol.Biol. / Year: 1981
Title: Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions.
Authors: Artymiuk, P.J. / Blake, C.C.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: X-Ray Studies of Water in Crystals of Lysozyme
Authors: Blake, C.C.F. / Pulford, W.C.A. / Artymiuk, P.J.
#2: Journal: Nature / Year: 1979
Title: Crystallographic Studies of the Dynamic Properties of Lysozyme
Authors: Artymiuk, P.J. / Blake, C.C.F. / Grace, D.E.P. / Oatley, S.J. / Phillips, D.C. / Sternberg, M.J.E.
#3: Journal: Atlas of Protein Sequence and Structure,Supplement 1
Year: 1973
History
DepositionOct 12, 1984Processing site: BNL
Revision 1.0Jan 2, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,7211
Polymers14,7211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.130, 60.990, 32.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HUMAN LYSOZYME


Mass: 14720.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61626, lysozyme
Has protein modificationY
Sequence detailsFOR PURPOSES OF COMPARISON WITH HEN EGG-WHITE LYSOZYME (HEWL) - HUMAN LYSOZYME HAS AN INSERTION OF ...FOR PURPOSES OF COMPARISON WITH HEN EGG-WHITE LYSOZYME (HEWL) - HUMAN LYSOZYME HAS AN INSERTION OF A GLYCINE BETWEEN HEWL RESIDUES 48 AND 49. THIS INSERTION IS LABELLED GLY 49 AND ALL SUBSEQUENT RESIDUE NUMBERS ARE HIGHER BY 1 THAN IN HEWL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.79 %
Crystal grow
*PLUS
Method: other / Details: Watson, H.C., (1963) Acta Cryst., A16, A81.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Num. obs: 18500

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Processing

RefinementResolution: 1.5→10 Å / Rfactor Rwork: 0.177 / Rfactor all: 0.187
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 0 0 1029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.05
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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