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
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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
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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;
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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
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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;
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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
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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;
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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
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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;
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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
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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;
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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
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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;
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