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- PDB-5lyt: COMPARISON OF RADIATION-INDUCED DECAY AND STRUCTURE REFINEMENT FR... -

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Entry
Database: PDB / ID: 5lyt
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: J.Mol.Biol. / Year: 1975
Title: An X-Ray Study of the Structure and Binding Properties of Iodine-Inactivated Lysozyme
Authors: Beddell, C.R. / Blake, C.C.F. / Oatley, S.J.
#2: Journal: J.Mol.Biol. / Year: 1974
Title: Real-Space Refinement of the Structure of Hen Egg-White Lysozyme
Authors: Diamond, R.
#3: Journal: Lysozyme / Year: 1974
Title: Crystallographic Studies of Lysozyme and its Interactions with Inhibitors and Substrates
Authors: Phillips, D.C.
#4: Journal: The Enzymes,Third Edition / Year: 1972
Title: Vertebrate Lysozymes
Authors: Imoto, T. / Johnson, L.N. / North, A.C.T. / Phillips, D.C. / Rupley, J.A.
#5: Journal: J.Mol.Biol. / Year: 1974
Title: Energy Refinement of Hen Egg-White Lysozyme
Authors: Levitt, M.
#6: Journal: J.Mol.Biol. / Year: 1974
Title: Crystal Structure of a Lysozyme-Tetrasaccharide Lactone Complex
Authors: Ford, L.O. / Johnson, L.N. / Machin, P.A. / Phillips, D.C. / Tjian, R.
#7: Journal: Proc.R.Soc.London,Ser.B / Year: 1967
Title: On the Conformation of the Hen Egg-White Lysozyme Molecule
Authors: Blake, C.C.F. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R.
#8: Journal: Proc.R.Soc.London,Ser.B / Year: 1967
Title: Crystallographic Studies of the Activity of Hen Egg-White Lysozyme
Authors: Blake, C.C.F. / Johnson, L.N. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R.
#9: Journal: Sci.Am. / Year: 1966
Title: The Three-Dimensional Structure of an Enzyme Molecule
Authors: Phillips, D.C.
#10: Journal: Nature / Year: 1965
Title: Structure of Hen Egg-White Lysozyme, a Three-Dimensional Fourier Synthesis at 2 Angstroms Resolution
Authors: Blake, C.C.F. / Koenig, D.F. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R.
#11: Journal: Nature / Year: 1965
Title: Structure of Some Crystalline Lysozyme-Inhibitor Complexes Determined by X-Ray Analysis at 6 Angstroms Resolution
Authors: Johnson, L.N. / Phillips, D.C.
#12: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#13: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMar 20, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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: HEN EGG WHITE LYSOZYME


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.420, 78.420, 36.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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.: 237 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
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: 5958 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.176

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.176 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 237 1238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
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: 0.176
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_d0.040.039
X-RAY DIFFRACTIONp_planar_d0.050.041
X-RAY DIFFRACTIONp_plane_restr0.0250.013
X-RAY DIFFRACTIONp_chiral_restr0.150.151
X-RAY DIFFRACTIONp_mcbond_it1.50.701
X-RAY DIFFRACTIONp_scbond_it21.087
X-RAY DIFFRACTIONp_mcangle_it21.086
X-RAY DIFFRACTIONp_scangle_it2.51.416

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