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- PDB-4lyt: COMPARISON OF RADIATION-INDUCED DECAY AND STRUCTURE REFINEMENT FR... -

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Basic information

Entry
Database: PDB / ID: 4lyt
TitleCOMPARISON OF RADIATION-INDUCED DECAY AND STRUCTURE REFINEMENT FROM X-RAY DATA COLLECTED FROM LYSOZYME CRYSTALS AT LOW AND AMBIENT TEMPERATURES
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: 1.9 Å
AuthorsDewan, J.C. / Young, A.C.M. / Tilton, R.F.
Citation
Journal: J.Appl.Crystallogr. / Year: 1993
Title: Comparison of Radiation-Induced Decay and Structure Refinement from X-Ray Data Collected from Lysozyme Crystals at Low and Ambient Temperatures
Authors: Young, A.C.M. / Dewan, J.C. / Nave, C. / Tilton, R.F.
#1: Journal: Acta Crystallogr.,Sect.C / Year: 1983
Title: Studies of Monoclinic Hen Egg White Lysozyme. II. The Refinement at 2.5 Angstroms Resolution-Conformational Variability between the Two Independent Molecules
Authors: Rao, S.T. / Hogle, J. / Sundaralingam, M.
#2: Journal: Thesis / Year: 1978
Title: The Structure of the Monoclinic Crystal Form of Hen Egg White Lysozyme at 2.5 Angstroms Resolution. Comparison of a Protein Structure in Several Crystalline Environments
Authors: Hogle, J.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1981
Title: Studies of Monoclinic Hen Egg White Lysozyme. I. Structure Solution at 4 Angstroms Resolution and Molecular-Packing Comparisons with Tetragonal and Triclinic Lysozymes
Authors: Hogle, J. / Rao, S.T. / Mallikarjunan, M. / Beddell, C. / Mcmullan, R.K. / Sundaralingam, M.
History
DepositionMar 20, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Oct 16, 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
B: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)28,6622
Polymers28,6622
Non-polymers00
Water3,441191
1
A: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.990, 62.920, 60.480
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEN EGG WHITE LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 2
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.: 191 / 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: 1.86 Å3/Da / Density % sol: 33.79 %
Crystal grow
*PLUS
Temperature: 293 K / pH: 4.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116.7 mg/mlprotein11
20.05 Macetate11
31 %11NaNO3
42 %12NaNO3

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. obs: 10739 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.179

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.179 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 0 191 2193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
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
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.040.033
X-RAY DIFFRACTIONp_planar_d0.050.034
X-RAY DIFFRACTIONp_plane_restr0.0250.012
X-RAY DIFFRACTIONp_chiral_restr0.150.131
X-RAY DIFFRACTIONp_mcbond_it1.50.697
X-RAY DIFFRACTIONp_scbond_it21.021
X-RAY DIFFRACTIONp_mcangle_it21.195
X-RAY DIFFRACTIONp_scangle_it2.51.555

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