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- PDB-1hnl: CRYSTAL STRUCTURE OF A GLUTATHIONYLATED HUMAN LYSOZYME: A FOLDING... -

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Basic information

Entry
Database: PDB / ID: 1hnl
TitleCRYSTAL STRUCTURE OF A GLUTATHIONYLATED HUMAN LYSOZYME: A FOLDING INTERMEDIATE MIMIC IN THE FORMATION OF A DISULFIDE BOND
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
GLUTATHIONE / Lysozyme C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsInaka, K. / Matsushima, M. / Miki, K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of a glutathionylated human lysozyme: a folding intermediate mimic in the formation of a disulfide bond.
Authors: Inaka, K. / Miki, K. / Kikuchi, M. / Taniyama, Y. / Matsushima, M.
#1: Journal: FEBS Lett. / Year: 1993
Title: Pdi and Glutathione-Mediated Reduction of the Glutathionylated Variant of Human Lysozyme
Authors: Hayano, T. / Inaka, K. / Otsu, M. / Taniyama, Y. / Miki, K. / Matsushima, M. / Masakazu, K.
History
DepositionDec 22, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9962
Polymers14,6891
Non-polymers3071
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.190, 60.960, 33.220
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: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Source detailsTHE EXPRESSION PLASMID OF THE MUTANT HUMAN LYSOZYME, C77A, IN WHICH CYS 77 IS REPLACED BY ALA, WAS ...THE EXPRESSION PLASMID OF THE MUTANT HUMAN LYSOZYME, C77A, IN WHICH CYS 77 IS REPLACED BY ALA, WAS PREVIOUSLY DESCRIBED (TANIYAMA,Y., SEKO,C., AND KIKUCHI,M. (1990) J.BIOL.CHEM. 265, 16767-16771).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal grow
*PLUS
Temperature: 293 K / pH: 6 / Method: unknown / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
22.5 M12NaCl
330 mMsodium phosphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 9501 / % possible obs: 84 %
Reflection
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 9999 Å / Num. measured all: 30257 / Rmerge(I) obs: 0.0667

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→5 Å /
RfactorNum. reflection
obs0.125 8230
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 20 113 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4251.5
X-RAY DIFFRACTIONp_mcangle_it2.3132
X-RAY DIFFRACTIONp_scbond_it2.2832
X-RAY DIFFRACTIONp_scangle_it3.5522.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1590.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.3
X-RAY DIFFRACTIONp_multtor_nbd0.1820.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2210.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor17.615
X-RAY DIFFRACTIONp_orthonormal_tor20.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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