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- PDB-2eql: CRYSTALLOGRAPHIC STUDIES OF A CALCIUM BINDING LYSOZYME FROM EQUIN... -

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Basic information

Entry
Database: PDB / ID: 2eql
TitleCRYSTALLOGRAPHIC STUDIES OF A CALCIUM BINDING LYSOZYME FROM EQUINE MILK AT 2.5 ANGSTROMS RESOLUTION
ComponentsHORSE MILK LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / metal ion 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
Lysozyme C, milk isozyme
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTsuge, H. / Ago, H. / Miyano, M.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1992
Title: Crystallographic studies of a calcium binding lysozyme from equine milk at 2.5 A resolution.
Authors: Tsuge, H. / Ago, H. / Noma, M. / Nitta, K. / Sugai, S. / Miyano, M.
#1: Journal: Biochim.Biophys.Acta / Year: 1991
Title: A Structural Study of Calcium-Binding Equine Lysozyme by Two-Dimensional 1H-NMR
Authors: Tsuge, H. / Koseki, K. / Miyano, M. / Shimazaki, K. / Chuman, T. / Matsumoto, T. / Noma, M. / Nitta, K. / Sugai, S.
#2: Journal: Biol.Chem.Hoppe-Seyler / Year: 1988
Title: Calcium-Binding Lysozymes
Authors: Nitta, K. / Tsuge, H. / Shimazaki, K. / Sugai, S.
#3: Journal: FEBS Lett. / Year: 1987
Title: The Calcium-Binding Property of Equine Lysozyme
Authors: Nitta, K. / Tsuge, H. / Sugai, S. / Shimazaki, K.
History
DepositionMay 27, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: 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

Downloads & links

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Assembly

Deposited unit
A: HORSE MILK LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,6741
Polymers14,6741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.100, 57.200, 38.700
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 HORSE MILK LYSOZYME


Mass: 14673.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P11376
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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
240 %Na citrate1drop
390 %Na citrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 4842 / Rmerge(I) obs: 0.039

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→7 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.234 -
obs0.234 4142
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 0 1023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg4.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Rfactor obs: 0.234 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 4.08

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