Start2Fold

The database of hydrogen/deuterium exchange data on protein folding and stability

Entry STF0006

Bacteriophage lambda lysozyme

 DOWNLOAD ENTRY IN XML

Protein information

Name of the protein: Endolysin
Organism: Escherichia phage lambda (Bacteriophage 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

 Show  Hide

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

 Show  Hide

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

 Show  Hide

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

 Show  Hide

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

 Show  Hide

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

 Show  Hide

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