Entry STF0006
Bacteriophage lambda lysozyme
Protein information
Name of the protein: | Endolysin |
Organism: | Escherichia phage lambda |
Number of residues: | 158 |
Related UniProt entry: | P03706 (Fragment: 1 - 158) |
Related PDB entry: | 1AM7 |
Visualize the data
Click here or on the image on the right to visualize the residues using JSmol. Warning: JSmol is known to load slowly on certain browsers, depending on the size of the macromolecule. The applet is optimized for Chrome, other browsers have limited support.
Experiment sets
EARLY
Method: Pulse labeling HDX NMR and MS
Conditions: pH 5.6; 20.0 Celsius; Probes: 54
Related publication:
PMID 20806781
Experiment details: "Samples were prepared using a QFM-5 rapid-mixing quenched-flow device. Standard pulse-labeling procedure was performed, in which deuterated unfolded lysozyme (5 mg/ml in 3 M Gdm2HCl and 500 mM DTT) was exposed to a high pH labeling pulse after various refolding periods (3.5-2000 ms) at 20 °C in 20 mM sodium acetate buffer, pH 5.6."
Protection threshold: refolding time constant < 180
Sequence:
MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV
CLICK TO DOWNLOAD SEQUENCE IN FASTA
EARLY residues
10: A;
11: F;
12: L;
14: M;
16: A;
18: S;
20: G;
21: T;
35: V;
41: L;
42: F;
64: A;
69: L;
74: W;
81: L;
83: L;
90: S;
91: Q;
96: L;
97: Q;
98: Q;
101: E;
102: R;
112: D;
117: I;
118: D;
146: F;
147: K;
152: T;
CLICK TO DOWNLOAD LIST OF RESIDUES
INTERMEDIATE
Method: Pulse labeling HDX NMR and MS
Conditions: pH 5.6; 20.0 Celsius; Probes: 54
Related publication:
PMID 20806781
Experiment details: "Samples were prepared using a QFM-5 rapid-mixing quenched-flow device. Standard pulse-labeling procedure was performed, in which deuterated unfolded lysozyme (5 mg/ml in 3 M Gdm2HCl and 500 mM DTT) was exposed to a high pH labeling pulse after various refolding periods (3.5-2000 ms) at 20 °C in 20 mM sodium acetate buffer, pH 5.6."
Protection threshold: 180 < refolding time constant < 200
Sequence:
MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV
CLICK TO DOWNLOAD SEQUENCE IN FASTA
INTERMEDIATE residues
9: K;
13: D;
15: L;
19: E;
93: A;
94: V;
95: A;
108: I;
109: D;
110: R;
119: R;
120: C;
144: A;
CLICK TO DOWNLOAD LIST OF RESIDUES
LATE
Method: Pulse labeling HDX NMR and MS
Conditions: pH 5.6; 20.0 Celsius; Probes: 54
Related publication:
PMID 20806781
Experiment details: "Samples were prepared using a QFM-5 rapid-mixing quenched-flow device. Standard pulse-labeling procedure was performed, in which deuterated unfolded lysozyme (5 mg/ml in 3 M Gdm2HCl and 500 mM DTT) was exposed to a high pH labeling pulse after various refolding periods (3.5-2000 ms) at 20 °C in 20 mM sodium acetate buffer, pH 5.6."
Protection threshold: refolding time constant > 200
Sequence:
MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV
CLICK TO DOWNLOAD SEQUENCE IN FASTA
LATE residues
8: R;
17: W;
33: Y;
67: Y;
68: Q;
78: R;
87: S;
92: D;
100: K;
116: A;
145: K;
148: E;
149: A;
151: G;
CLICK TO DOWNLOAD LIST OF RESIDUES
STRONG
Method: Native exchange NMR
Conditions: pH 4.4-5.6; 20.0 Celsius; Probes: 66
Related publication:
PMID 20806781
Experiment details: "H/D exchange rates were measured using 2 mM 15N-labeled enzyme, on the basis of published resonance assignments. Exchange was initiated by a 10-fold dilution of a 2 mM 15N-labeled protein sample in 10 mM HEPES, pH 7.0, into a D2O solution at pH 5.6 or 4.4. Samples were subsequently concentrated 10-fold by ultrafiltration at 4 °C to give a final protein concentration of 2 mM; this procedure was repeated five times. Following exchange and concentration, the protein sample was subsequently analyzed by 2D NMR."
Protection threshold: log(P) > 5
Sequence:
MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV
CLICK TO DOWNLOAD SEQUENCE IN FASTA
STRONG residues
11: F;
12: L;
14: M;
15: L;
17: W;
18: S;
19: E;
21: T;
35: V;
67: Y;
69: L;
92: D;
93: A;
94: V;
96: L;
97: Q;
98: Q;
99: I;
100: K;
108: I;
117: I;
120: C;
CLICK TO DOWNLOAD LIST OF RESIDUES
MEDIUM
Method: Native exchange NMR
Conditions: pH 4.4-5.6; 20.0 Celsius; Probes: 66
Related publication:
PMID 20806781
Experiment details: "H/D exchange rates were measured using 2 mM 15N-labeled enzyme, on the basis of published resonance assignments. Exchange was initiated by a 10-fold dilution of a 2 mM 15N-labeled protein sample in 10 mM HEPES, pH 7.0, into a D2O solution at pH 5.6 or 4.4. Samples were subsequently concentrated 10-fold by ultrafiltration at 4 °C to give a final protein concentration of 2 mM; this procedure was repeated five times. Following exchange and concentration, the protein sample was subsequently analyzed by 2D NMR."
Protection threshold: 3 < log(P) < 5
Sequence:
MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV
CLICK TO DOWNLOAD SEQUENCE IN FASTA
MEDIUM residues
9: K;
10: A;
16: A;
20: G;
33: Y;
36: I;
42: F;
64: A;
65: G;
66: R;
68: Q;
74: W;
77: Y;
87: S;
90: S;
91: Q;
95: A;
109: D;
110: R;
112: D;
116: A;
119: R;
124: W;
144: A;
145: K;
146: F;
147: K;
148: E;
149: A;
CLICK TO DOWNLOAD LIST OF RESIDUES
WEAK
Method: Native exchange NMR
Conditions: pH 4.4-5.6; 20.0 Celsius; Probes: 66
Related publication:
PMID 20806781
Experiment details: "H/D exchange rates were measured using 2 mM 15N-labeled enzyme, on the basis of published resonance assignments. Exchange was initiated by a 10-fold dilution of a 2 mM 15N-labeled protein sample in 10 mM HEPES, pH 7.0, into a D2O solution at pH 5.6 or 4.4. Samples were subsequently concentrated 10-fold by ultrafiltration at 4 °C to give a final protein concentration of 2 mM; this procedure was repeated five times. Following exchange and concentration, the protein sample was subsequently analyzed by 2D NMR."
Protection threshold: log(P) < 3
Sequence:
MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVREIDV
CLICK TO DOWNLOAD SEQUENCE IN FASTA
WEAK residues
8: R;
32: G;
41: L;
75: D;
76: A;
78: R;
81: L;
83: L;
101: E;
102: R;
118: D;
127: L;
142: L;
151: G;
152: T;
CLICK TO DOWNLOAD LIST OF RESIDUES