PDBsum entry: 193l

Hydrolase (o-glycosyl)

PDB id: 193l

Contents

Protein chain

129 a.a. *

Metals

_NA

_CL

Waters ×142

* Residue conservation analysis

PDB id:

193l

Name:

Hydrolase (o-glycosyl)

Title:

The 1.33 a structure of tetragonal hen egg white lysozyme

Structure:

Lysozyme. Chain: a

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Cellular_location: egg white

Resolution:

1.33Å R-factor: 0.184 R-free: 0.226

Authors:

M.C.Vaney,S.Maignan,M.Ries-Kautt,A.Ducruix

Key ref:

M.C.Vaney et al. (1996). High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Acta Crystallogr D Biol Crystallogr, 52, 505-517. PubMed id: 15299672 DOI: 10.1107/S090744499501674X

Date:

01-Sep-95 Release date: 07-Dec-95

Protein chain

P00698  (LYSC_CHICK) -  Lysozyme C

Seq: 147 a.a.

Struc: 129 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.17 - Lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (5 terms)

DOI no: 10.1107/S090744499501674X

Acta Crystallogr D Biol Crystallogr 52:505-517 (1996)

PubMed id: 15299672

High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission.

M.C.Vaney, S.Maignan, M.Riès-Kautt, A.Ducriux.

ABSTRACT

Crystals of tetragonal hen egg-white lysozyme were grown using Advanced Protein Crystallization Facility (APCF) apparatus under a microgravity environment (SpaceHab-01 mission) and ground control conditions. Crystals were grown from NaCl as a crystallizing agent at pH 4.3. The X-ray diffraction patterns of the best diffracting ground- and space-grown crystals were recorded using synchrotron radiation and an image plate on the W32 beamline at LURE. Both ground- and space-grown crystals showed nearly equivalent maximum resolution of 1.3-1.4 A. Refinements were carried out with the program X-PLOR with final R values of 18.45 and 18.27% for structures from ground- and space- grown crystals, respectively. The two structures are nearly identical with the root-mean-square difference on all protein atoms being 0.13 A. Some residues of the two refined structures show multiple alternative conformations. Two ions were localized into the electron-density maps of the two structures: one chloride ion at the interface between two symmetry-related molecules and one sodium ion stabilizing the loop Ser60-Leu75. The sodium ion is surrounded by six ligands which form a bipyramid around it at distances of 2.2-2.6 A.

Selected figure(s)

Figure 4.
Fig. 4. Stereoview of the overall lysozyme ground structure. The Na + ion is located inside the loop 60-73 and the interactions are symolized by the dashed lines. The CI- on is localized at the interface of two molecules and is at a distance of about 24/k from the Na + ion for ground and space structures). All the diagrams were prodced using the program MOLSCRIPT (Kraulis, 1991).

Figure 6.
ig. 6. Stereoscopic views for the ground structure of the final 1Fol -IFcl electron-density ap at 1.33/~ resolution with the contour level at ltr: the issing density is observed round some atoms of the esidue Trp62 while the high quality of the map shows the quasi-atomic resolution round residue Trp63. The space struture shows similar conformations and qualities of he map.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 505-517) copyright 1996.

Figures were selected by an automated process.