Start2Fold

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

Entry STF0021

Bacteriophage T4 lysozyme

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Protein information

Name of the protein: Lysozyme
Organism: Enterobacteria phage T4 (Bacteriophage T4)
Number of residues: 164
Related UniProt entry:   D9IEF7 (Fragment: 1 - 164)
Related PDB entry:   2LZM

Visualize the data

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Experiment sets

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EARLY

Method: Dead time pulse labeling HDX NMR

Conditions: pH 10.2; 25.0 Celsius; Probes: 60

Related publication:
 PMID 17097105

Experiment details: "Dead-time pulse-labeling experiment, in which the unfolded protein sample in D2O and 8.5 M D-urea was mixed with a H2O solution at pH 10.2 by a ratio of 1:9. After 13 ms, the sample was quenched at pH 3.0. At pH 10.2 and 25 °C, unprotected amide deuterons can exchange with solvent protons in less than 1 ms."

Protection threshold: proton occupancy < 0.6

Sequence: MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
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EARLY residues

7: L; 71: V; 79: L; 98: A; 102: M; 103: V; 104: F;
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INTERMEDIATE

Method: Dead time pulse labeling HDX NMR

Conditions: pH 10.2; 25.0 Celsius; Probes: 60

Related publication:
 PMID 17097105

Experiment details: "Dead-time pulse-labeling experiment, in which the unfolded protein sample in D2O and 8.5 M D-urea was mixed with a H2O solution at pH 10.2 by a ratio of 1:9. After 13 ms, the sample was quenched at pH 3.0. At pH 10.2 and 25 °C, unprotected amide deuterons can exchange with solvent protons in less than 1 ms."

Protection threshold: 0.6 < proton occupancy < 0.8

Sequence: MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

INTERMEDIATE residues

4: F; 64: E; 74: A; 78: I; 81: N; 84: L; 97: A;
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STRONG

Method: Native exchange NMR

Conditions: pH 6.0; 25.0 Celsius; Probes: 114

Related publication:
 PMID 10542101

Experiment details: "The exchange of 114 of the 164 backbone amide protons in T4 lysozyme was monitored as a function of denaturant concentration (eleven samples between 0 M and 2 M GdmCl). Exchange was initiated by spinning the samples through a Quick-sep spin column packed with G-25 resin pre-equilibrated in deuterated buffer (50 mM sodium phosphate, pD 6.0, 0.1 M KCl) with varying amounts of per-deuterated GdmCl. All of these denaturant concentrations are below the folding transition measured by global probes. Exchange was measured by two-dimensional 1H-15N HSQC spectra taken over a period of hours to months."

Protection threshold: ΔG(op)(kcal/mol) > 15

Sequence: MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

5: E; 7: L; 10: D; 66: L; 71: V; 72: D; 73: A; 74: A; 76: R; 79: L; 85: K; 96: R; 97: A; 98: A; 99: L; 100: I; 101: N; 102: M; 103: V; 104: F; 105: Q; 106: M; 121: L; 123: Q; 147: K; 149: V; 153: F;
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MEDIUM

Method: Native exchange NMR

Conditions: pH 6.0; 25.0 Celsius; Probes: 114

Related publication:
 PMID 10542101

Experiment details: "The exchange of 114 of the 164 backbone amide protons in T4 lysozyme was monitored as a function of denaturant concentration (eleven samples between 0 M and 2 M GdmCl). Exchange was initiated by spinning the samples through a Quick-sep spin column packed with G-25 resin pre-equilibrated in deuterated buffer (50 mM sodium phosphate, pD 6.0, 0.1 M KCl) with varying amounts of per-deuterated GdmCl. All of these denaturant concentrations are below the folding transition measured by global probes. Exchange was measured by two-dimensional 1H-15N HSQC spectra taken over a period of hours to months."

Protection threshold: 13 < ΔG(op)(kcal/mol) < 15

Sequence: MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

MEDIUM residues

6: M; 8: R; 9: I; 11: E; 75: V; 80: R; 84: L; 88: Y; 91: L; 112: A; 122: Q; 131: V; 150: I; 151: T; 152: T; 154: R; 156: G; 157: T; 161: Y;
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WEAK

Method: Native exchange NMR

Conditions: pH 6.0; 25.0 Celsius; Probes: 114

Related publication:
 PMID 10542101

Experiment details: "The exchange of 114 of the 164 backbone amide protons in T4 lysozyme was monitored as a function of denaturant concentration (eleven samples between 0 M and 2 M GdmCl). Exchange was initiated by spinning the samples through a Quick-sep spin column packed with G-25 resin pre-equilibrated in deuterated buffer (50 mM sodium phosphate, pD 6.0, 0.1 M KCl) with varying amounts of per-deuterated GdmCl. All of these denaturant concentrations are below the folding transition measured by global probes. Exchange was measured by two-dimensional 1H-15N HSQC spectra taken over a period of hours to months."

Protection threshold: 11 < ΔG(op)(kcal/mol) < 13

Sequence: MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

WEAK residues

4: F; 14: R; 67: F; 70: D; 129: A; 130: A; 155: T;
 CLICK TO DOWNLOAD LIST OF RESIDUES