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- PDB-1lzt: REFINEMENT OF TRICLINIC LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1lzt
TitleREFINEMENT OF TRICLINIC LYSOZYME
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: 1.97 Å
AuthorsHodsdon, J.M. / Brown, G.M. / Sieker, L.C. / Jensen, L.H.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Refinement of triclinic lysozyme: I. Fourier and least-squares methods.
Authors: Hodsdon, J.M. / Brown, G.M. / Sieker, L.C. / Jensen, L.H.
#1: Journal: J.Mol.Biol. / Year: 1976
Title: Structures of Triclinic Mono-and Di-N-Acetylglucosamine. Lysozyme Complexes-A Crystallographic Study
Authors: Kurachi, K. / Sieker, L.C. / Jensen, L.H.
History
DepositionApr 1, 1985Processing site: BNL
Revision 1.0Jul 18, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)14,3311
Polymers14,3311
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.283, 31.980, 34.291
Angle α, β, γ (deg.)88.53, 108.57, 111.85
Int Tables number1
Space group name H-MP1
Atom site foot note1: SEE REMARK 5.

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Components

#1: Protein HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal grow
*PLUS
pH: 4.55 / Method: unknown / Details: pH is adjusted to 4.55 with 0.1M scetic acid
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %protein11
22 %11NaNO3
30.05 M11sodium acetate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.54 Å / Num. obs: 7838

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Processing

SoftwareName: SHARP / Classification: phasing
RefinementResolution: 1.97→10 Å
Details: RESIDUES 101 THROUGH 103 ARE GENERALLY PROPERLY POSITIONED BUT THE ELECTRON DENSITY IS NOT SHARP HERE. DETAILED ANALYSIS OF THIS REGION SHOULD BE DONE VERY CAUTIOUSLY.
RfactorNum. reflection
Rwork0.254 -
obs-7142
Refinement stepCycle: LAST / Resolution: 1.97→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 220 1221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0298
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg8.67
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d5.35
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
Highest resolution: 1.97 Å / Lowest resolution: 10 Å / Num. reflection obs: 7142 / Rfactor obs: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d

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