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- PDB-4lym: CRYSTAL STRUCTURE OF LOW HUMIDITY TETRAGONAL LYSOZYME AT 2.1-ANGS... -

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Basic information

Entry
Database: PDB / ID: 4lym
TitleCRYSTAL STRUCTURE OF LOW HUMIDITY TETRAGONAL LYSOZYME AT 2.1-ANGSTROMS RESOLUTION. VARIABILITY IN HYDRATION SHELL AND ITS STRUCTURAL CONSEQUENCES
ComponentsHEN EGG WHITE LYSOZYME
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 / Resolution: 2.1 Å
AuthorsKodandapani, R. / Suresh, C.G. / Vijayan, M.
Citation
Journal: J.Biol.Chem. / Year: 1990
Title: Crystal structure of low humidity tetragonal lysozyme at 2.1-A resolution. Variability in hydration shell and its structural consequences.
Authors: Kodandapani, R. / Suresh, C.G. / Vijayan, M.
#1: Journal: Curr.Sci. / Year: 1991
Title: Rigid and Flexible Regions in Lysozyme and the Invariant Features in its Hydration Shell
Authors: Madhusudhan / Vijayan, M.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1985
Title: Water-Mediated Transformations in Protein Crystals
Authors: Salunke, D.M. / Veerapandian, B. / Kodandapani, R. / Vijayan, M.
#3: Journal: Curr.Sci. / Year: 1984
Title: Water-Mediated Structural Transformations in a New Crystal Form of Ribonucleasea and Tetragonal Lysozyme
Authors: Salunke, D.M. / Veerapandian, B. / Vijayan, M.
History
DepositionJul 30, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Oct 30, 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: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.400, 78.400, 37.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: THE PORTION OF THE PEPTIDE CHAIN FORMING THE LOOP (PRO 70 TO ARG 73) AND THE C-TERMINAL RESIDUES ARG 128 AND LEU 129 ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS.
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

21A-171-

HOH

31A-198-

HOH

41A-200-

HOH

51A-228-

HOH

61A-233-

HOH

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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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal
*PLUS
Density % sol: 37.8 %
Crystal grow
*PLUS
pH: 4.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.04 Macetate11
25 %11NaCl

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 7127 / Num. measured all: 68244 / Rmerge(I) obs: 0.163

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→10 Å / σ(F): 2
Details: THE PORTION OF THE PEPTIDE CHAIN FORMING THE LOOP (PRO 70 TO ARG 73) AND THE C-TERMINAL RESIDUES ARG 128 AND LEU 129 ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS.
RfactorNum. reflection
obs0.1623 6269
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 157 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0570.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0660.06
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_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1370.12
X-RAY DIFFRACTIONp_singtor_nbd0.1980.5
X-RAY DIFFRACTIONp_multtor_nbd0.2920.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.250.5
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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