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- PDB-1lhm: THE CRYSTAL STRUCTURE OF A MUTANT LYSOZYME C77(SLASH)95A WITH INC... -

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Basic information

Entry
Database: PDB / ID: 1lhm
TitleTHE CRYSTAL STRUCTURE OF A MUTANT LYSOZYME C77(SLASH)95A WITH INCREASED SECRETION EFFICIENCY IN YEAST
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.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: The crystal structure of a mutant human lysozyme C77/95A with increased secretion efficiency in yeast.
Authors: Inaka, K. / Taniyama, Y. / Kikuchi, M. / Morikawa, K. / Matsushima, M.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1988
Title: Role of Disulfide Bonds in Folding and Secretion of Human Lysozyme in Saccharomyces Cerevisiae
Authors: Taniyama, Y. / Yamamoto, Y. / Kikuchi, N.Nakao M. / Ikehara, M.
History
DepositionOct 2, 1991Processing site: BNL
Revision 1.0Apr 15, 1992Provider: 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 1.4Nov 20, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,6571
Polymers14,6571
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.610, 60.850, 33.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE CYS 77 - CYS 95 DISULFIDE BOND HAS BEEN DELETED IN THIS ENTRY.

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Components

#1: Protein HUMAN LYSOZYME


Mass: 14656.562 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.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CYS 77 - CYS 95 DISULFIDE BOND HAS BEEN DELETED IN THIS ENTRY.
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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal grow
*PLUS
Temperature: 13.0 ℃ / Method: unknown / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein11
22.5 M11NaCl
330 mMsodium phosphate11pH6.0

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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: 11241 / Num. measured all: 78240 / Rmerge(I) obs: 0.0834

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.16 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 0 101 1128
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 5 Å / Num. reflection obs: 10370 / Rfactor obs: 0.163 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.140.02
X-RAY DIFFRACTIONp_angle_d0.0360.035
X-RAY DIFFRACTIONp_mcbond_it0.9771.5
X-RAY DIFFRACTIONp_scbond_it1.9732
X-RAY DIFFRACTIONp_mcangle_it1.4812
X-RAY DIFFRACTIONp_scangle_it3.0842.5
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1370.15

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