Entry STF0021
Bacteriophage T4 lysozyme
Protein information
| Name of the protein: | Lysozyme |
| Organism: | Enterobacteria phage T4 |
| Number of residues: | 164 |
| Related UniProt entry: | D9IEF7 (Fragment: 1 - 164) |
| Related PDB entry: | 2LZM |
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: 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
CLICK TO DOWNLOAD SEQUENCE IN FASTA
EARLY residues
7: L;
71: V;
79: L;
98: A;
102: M;
103: V;
104: F;
CLICK TO DOWNLOAD LIST OF RESIDUES
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;
CLICK TO DOWNLOAD LIST OF RESIDUES
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;
CLICK TO DOWNLOAD LIST OF RESIDUES
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;
CLICK TO DOWNLOAD LIST OF RESIDUES
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