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- PDB-193l: THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 193l
TitleTHE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME
ComponentsLYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / SYNCHROTRON / Resolution: 1.33 Å
AuthorsVaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducruix, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission.
Authors: Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducriux, A.
#1: Journal: To be Published
Title: Effect of Microgravity on Rate of Nucleation, Size and Quality of Lysozyme Crystals Grown in the Advanced Protein Crystallization Facility on Spacehab-01
Authors: Ries-Kautt, M.M. / Broutin, I. / Ducruix, A.F. / Shephard, W. / Kahn, R. / Lorber, B. / Theobald, A. / Giege, R. / Chayen, N. / Blow, D. / Paal, K. / Littke, W.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Thermal Expansion of Hen-Egg-White Lysozyme. Comparison of the 1.9 Angstroms Resolution Structures of the Tetragonal Form of the Enzyme at 100K and 298K
Authors: Young, A.C.M. / Tilton, R.F. / Dewan, J.C.
#3: Journal: J.Cryst.Growth / Year: 1992
Title: Experiment and Equipment for Protein Crystallization in Microgram Facilities
Authors: Bosch, R. / Lautenschlager, P. / Potthast, L. / Stapelmann, J.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3903
Polymers14,3311
Non-polymers582
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.540, 78.540, 37.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-272-

HOH

21A-273-

HOH

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Components

#1: Protein LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: EGG WHITE / References: UniProt: P00698
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growpH: 4.3 / Details: pH 4.3
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein 11
21.65 M12NaCl
350 mMNa acetate12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901 Å
DetectorType: MARRESEARCH / Date: Sep 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 1.33→15 Å / Num. obs: 24111 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.031
Reflection
*PLUS
Rmerge(I) obs: 0.031 / Biso Wilson estimate: 14.7 Å2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.33→7 Å / σ(F): 0
Details: SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG 21, ARG 61, TRP 62, ARG 73 ASN 77, LYS 97, ASP 101, ASN 103, GLN 121, ARG 125, AND LEU 129 HAVE A POORLY DEFINED DENSITY. THESE ATOMS WERE BUILT ...Details: SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG 21, ARG 61, TRP 62, ARG 73 ASN 77, LYS 97, ASP 101, ASN 103, GLN 121, ARG 125, AND LEU 129 HAVE A POORLY DEFINED DENSITY. THESE ATOMS WERE BUILT USING STEREOCHEMICAL CONSTRAINTS AND KEPT IN THE COORDINATE FILE. WATER MOLECULES 272 AND 273 ARE ON A TWO-FOLD AXIS AND HAVE BEEN MODELED WITH 50% OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.226 -10 %
Rwork0.184 --
obs0.184 23910 -
Displacement parametersBiso mean: 19.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.33→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 2 142 1156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.478
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.26
X-RAY DIFFRACTIONx_improper_angle_deg

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