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- PDB-2lz2: THE THREE DIMENSIONAL STRUCTURE OF TURKEY EGG WHITE LYSOZYME AT 2... -

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Basic information

Entry
Database: PDB / ID: 2lz2
TitleTHE THREE DIMENSIONAL STRUCTURE OF TURKEY EGG WHITE LYSOZYME AT 2.2 ANGSTROMS RESOLUTION
ComponentsTURKEY EGG WHITE LYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


glycosaminoglycan binding / 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 / 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 speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsParsons, M.R. / Phillips, S.E.V.
CitationJournal: To be Published
Title: The Three Dimensional Structure of Turkey Egg White Lysozyme at 2.2 Angstroms Resolution
Authors: Parsons, M.R. / Phillips, S.E.V.
History
DepositionOct 20, 1988Processing site: BNL
Revision 1.0Oct 15, 1989Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TURKEY EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,2281
Polymers14,2281
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.000, 71.000, 84.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: SEE REMARK 5.

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Components

#1: Protein TURKEY EGG WHITE LYSOZYME


Mass: 14228.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / References: UniProt: P00703, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.17 Å3/Da / Density % sol: 43.33 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→10 Å / Rfactor obs: 0.192
Details: PRO 70, GLY 71, AND SER 72 DO NOT MAKE A GOOD FIT TO THE ELECTRON DENSITY AND HAVE HIGH TEMPERATURE FACTORS. THIS REGION IS THOUGHT TO BE FLEXIBLE.
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 0 111 1105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.028
X-RAY DIFFRACTIONp_angle_d0.092
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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