1. The three-dimensional structure of PNGase F, a glycosyl asparaginase from Flavobacterium meningosepticum 
Gillian E Norris, Timothy J Stillman, Bryan F Anderson, Edward N Baker 
Structure 
Volume 2, Issue 11, Pages (November 1994)
DOI: /S (94)

2. Figure 1
Part of the 2.5 Å electron density map from which the initial model for PNGase F was determined, showing extended strands characteristic of the all-β structure (here fitted with the initial polyalanine trace). Contours are at 1.0σ.
Structure 1994 2, DOI: ( /S (94) )

3. Figure 2
Ramachandran plot for the refined atomic model of PNGase F. Triangles represent glycine residues and squares represent non-glycine residues. Of the residues 4–314, 90% are in the most favoured regions [51] and only Trp86 is in a normally disallowed region (see text).
Structure 1994 2, DOI: ( /S (94) )

4. Figure 3
Two regions of the final 2|Fo|–|Fc| electron density map, calculated at 1.8 Å resolution, using the refined model phases, and contoured at 1.5σ . (a) Part of the β-sheet structure of domain 1 with hydrogen bonds indicated by dashes. (b) The environment of Tyr85 and Trp86 in the cleft at the top of the molecule. The 1–3 hydrogen bond of theγ-turn 85–87 is identified by a dashed line.
Structure 1994 2, DOI: ( /S (94) )

5. Figure 3
Two regions of the final 2|Fo|–|Fc| electron density map, calculated at 1.8 Å resolution, using the refined model phases, and contoured at 1.5σ . (a) Part of the β-sheet structure of domain 1 with hydrogen bonds indicated by dashes. (b) The environment of Tyr85 and Trp86 in the cleft at the top of the molecule. The 1–3 hydrogen bond of theγ-turn 85–87 is identified by a dashed line.
Structure 1994 2, DOI: ( /S (94) )

6. Figure 4
(a) Stereo Cα plot of the PNGase F molecule. Domain 1 is on the right and domain 2 is on the left. In this orientation the connection between the two domains is at the bottom and one of the putative active site clefts is at the top of the molecule. (b) A schematic diagram (drawn with RIBBONS [52] ) showing domain 1 in green, domain 2 in red, and the interdomain connection and disulphide bonds in yellow. The two domain-2 loops that reach across to interact with domain 1, 151–159 and 227–257, are shown in blue and orange respectively.
Structure 1994 2, DOI: ( /S (94) )

7. Figure 4
(a) Stereo Cα plot of the PNGase F molecule. Domain 1 is on the right and domain 2 is on the left. In this orientation the connection between the two domains is at the bottom and one of the putative active site clefts is at the top of the molecule. (b) A schematic diagram (drawn with RIBBONS [52] ) showing domain 1 in green, domain 2 in red, and the interdomain connection and disulphide bonds in yellow. The two domain-2 loops that reach across to interact with domain 1, 151–159 and 227–257, are shown in blue and orange respectively.
Structure 1994 2, DOI: ( /S (94) )

8. Figure 5
Topology of the PNGase F molecule, with domain 1 on left and domain 2 on right. The β-strands are identified using the convention adopted for the viral coat proteins [23] and the residue numbers associated with each strand are given. The inset shows the classic eight-stranded β jelly roll motif for comparison.
Structure 1994 2, DOI: ( /S (94) )

9. Figure 6
The two possible active site regions in the PNGase F molecule. The orientation and colouring are as in Figure 4a. Some potential hydrogen bonds are shown in white. Site 1 (at the bottom of the molecule in this orientation) comprises two threonine residues, Thr42 and Thr101 (orange), together with Lys44 (dark blue) and Asp99 (red), all near the bottom of domain 1, facing the concave side of the domain 2 β-sandwich. Site 2 is found in a cleft at the top of the molecule, flanked with aromatic residues; five tryptophans (light blue) and one phenylalanine (dark blue). Also shown are a projecting histidine residue, His193 (magenta), and, at the bottom of the cleft, two acidic residues Asp60 and Glu206 (red) and their connecting water molecule (pink), together with Tyr85 (orange) and Arg248 (dark blue). (Figure drawn with RIBBONS [52]).
Structure 1994 2, DOI: ( /S (94) )

10. Figure 7
Stereoviews of the residues in the two potential active site clefts (see text). (a) The hydrogen bonded trio, Thr101, Asp99 and Lys44, with the nearby Thr42 (see also Figure 6a). (b) The surroundings of the two acidic residues, Asp60 and Glu206 at the floor of the top cleft (see also Figure 6a).
Structure 1994 2, DOI: ( /S (94) )

11. Figure 7
Stereoviews of the residues in the two potential active site clefts (see text). (a) The hydrogen bonded trio, Thr101, Asp99 and Lys44, with the nearby Thr42 (see also Figure 6a). (b) The surroundings of the two acidic residues, Asp60 and Glu206 at the floor of the top cleft (see also Figure 6a).
Structure 1994 2, DOI: ( /S (94) )

12. Figure 8
(a) The amino-terminal and (b) the carboxy-terminal β jelly roll domains of PNGase F viewed edge-on to the β-sandwich structures. These domains are compared with several other jelly roll structures, (c) 1,3–1,4-β-glucanase [8],(d) bovine S-lectin [41] and (e) coral tree lectin (1LTE). The locations of bound substrate for the latter three structures are also shown. More extensive comparisons of lectin domains are in [11]. (Diagrams drawn with MOLSCRIPT [53]).
Structure 1994 2, DOI: ( /S (94) )

13. Figure 8
(a) The amino-terminal and (b) the carboxy-terminal β jelly roll domains of PNGase F viewed edge-on to the β-sandwich structures. These domains are compared with several other jelly roll structures, (c) 1,3–1,4-β-glucanase [8],(d) bovine S-lectin [41] and (e) coral tree lectin (1LTE). The locations of bound substrate for the latter three structures are also shown. More extensive comparisons of lectin domains are in [11]. (Diagrams drawn with MOLSCRIPT [53]).
Structure 1994 2, DOI: ( /S (94) )