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- PDB-1lz4: ENTHALPIC DESTABILIZATION OF A MUTANT HUMAN LYSOZYME LACKING A DI... -

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Basic information

Entry
Database: PDB / ID: 1lz4
TitleENTHALPIC DESTABILIZATION OF A MUTANT HUMAN LYSOZYME LACKING A DISULFIDE BRIDGE BETWEEN CYSTEINE-77 AND CYSTEINE-95
ComponentsHUMAN LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
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 / Resolution: 1.8 Å
AuthorsInaka, K. / Matsushima, M. / Kuroki, R. / Taniyama, Y. / Kikuchi, M.
Citation
Journal: Biochemistry / Year: 1992
Title: Enthalpic destabilization of a mutant human lysozyme lacking a disulfide bridge between cysteine-77 and cysteine-95.
Authors: Kuroki, R. / Inaka, K. / Taniyama, Y. / Kidokoro, S. / Matsushima, M. / Kikuchi, M. / Yutani, K.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: The Crystal Structure of a Mutant Human Lysozyme C77(Slash)95A with Increased Secretion Efficiency in Yeast
Authors: Inaka, K. / Taniyama, Y. / Kikuchi, M. / Morikawa, K. / Matsushima, M.
History
DepositionFeb 3, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)14,6891
Polymers14,6891
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.820, 60.860, 33.330
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: 14688.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61626, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal grow
*PLUS
Temperature: 13.0 ℃ / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
22.5 M1reservoirNaCl
330 mMsodium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 9999 Å / Num. obs: 11258 / Num. measured all: 40579 / Rmerge(I) obs: 0.0556

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→5 Å
Details: THE ELECTRON DENSITIES OF THE LOOP BETWEEN ALA 73 AND HIS 78 ARE VERY WEAK AND THE ATOMS OF THE LOOP HAVE LARGE B FACTORS. THEN THE LOOP CAN BE VERY FLEXIBLE.
RfactorNum. reflection
obs0.188 10265
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 0 57 1073
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 5 Å / Num. reflection obs: 10265 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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