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- PDB-2lym: CRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME AT A HYDROSTATIC PRES... -

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Basic information

Entry
Database: PDB / ID: 2lym
TitleCRYSTAL STRUCTURE OF HEN EGG-WHITE LYSOZYME AT A HYDROSTATIC PRESSURE OF 1000 ATMOSPHERES
ComponentsHEN EGG WHITE LYSOZYME
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 Å
AuthorsKundrot, C.E. / Richards, F.M.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres.
Authors: Kundrot, C.E. / Richards, F.M.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Effect of Hydrostatic Pressure on the Solvent in Crystals of Hen Egg-White Lysozyme
Authors: Kundrot, C.E. / Richards, F.M.
#2: Journal: J.Appl.Crystallogr. / Year: 1986
Title: Collection and Processing of X-Ray Diffraction Data from Protein Crystals at High Pressure
Authors: Kundrot, C.E. / Richards, F.M.
History
DepositionJun 8, 1987Processing site: BNL
Revision 1.0Oct 16, 1987Provider: 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

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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
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.170, 79.170, 37.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: SEE REMARK 4.

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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 / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal grow
*PLUS
pH: 4.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.02 Macetate11
20.83 M11NaCl

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→79.1 Å / Rfactor obs: 0.149 / σ(F): 1
Details: THE RMS DEVIATION BETWEEN THE 1 ATM, 1.4 M NACL STRUCTURE PRESENTED IN THIS ENTRY AND THE HIGHLY REFINED TETRAGONAL HEWL LYSOZYME STRUCTURE OBTAINED FROM CRYSTALS SURROUNDED BY 0.8 M NACL, 0. ...Details: THE RMS DEVIATION BETWEEN THE 1 ATM, 1.4 M NACL STRUCTURE PRESENTED IN THIS ENTRY AND THE HIGHLY REFINED TETRAGONAL HEWL LYSOZYME STRUCTURE OBTAINED FROM CRYSTALS SURROUNDED BY 0.8 M NACL, 0.02 M SODIUM ACETATE BUFFER, PH 4.7 (ARTYMIUK ET AL., TO BE PUBLISHED) IS 0.19 ANGSTROMS FOR MAIN CHAIN ATOMS (N, CA, C, O, CB).
Refinement stepCycle: LAST / Resolution: 2→79.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 151 1152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.032
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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