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- PDB-132l: STRUCTURAL CONSEQUENCES OF REDUCTIVE METHYLATION OF LYSINE RESIDU... -

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Basic information

Entry
Database: PDB / ID: 132l
TitleSTRUCTURAL CONSEQUENCES OF REDUCTIVE METHYLATION OF LYSINE RESIDUES IN HEN EGG WHITE LYSOZYME: AN X-RAY ANALYSIS AT 1.8 ANGSTROMS RESOLUTION
ComponentsHEN EGG WHITE LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsRayment, I. / Rypniewski, W.R. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1993
Title: Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: an X-ray analysis at 1.8-A resolution.
Authors: Rypniewski, W.R. / Holden, H.M. / Rayment, I.
History
DepositionJun 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,4941
Polymers14,4941
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.600, 56.300, 73.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: ATOM NZ OF LYS 1 HAS BEEN DIMETHYLATED AND THE N-TERMINUS HAS BEEN DIMETHYLATED.
2: ATOM NZ OF LYS 13, LYS 33, LYS 96, AND LYS 116 HAS BEEN DIMETHYLATED.

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Components

#1: Protein HEN EGG WHITE LYSOZYME


Mass: 14494.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.08 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.68 Å / Num. obs: 4844 / % possible obs: 93.6 % / Observed criterion σ(I): 3 / Num. measured all: 19165 / Rmerge(I) obs: 0.057

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.8→30 Å /
RfactorNum. reflection
obs0.173 10796
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 0 78 1091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg1.79
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 10796 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d15.623
X-RAY DIFFRACTIONt_plane_restr0.017

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