Entry STF0002
E. coli apo-maltose binding protein (apo-MBP)
Protein information
| Name of the protein: | Maltose-binding periplasmic protein |
| Organism: | Escherichia coli (strain K12) |
| Number of residues: | 370 |
| Related UniProt entry: | P0AEX9 (Fragment: 27 - 396) |
| Related PDB entry: | 1OMP |
Visualize the data
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Experiment sets
EARLY
Method: Pulse labeling HDX MS
Conditions: pH 9.0; 20.0 Celsius; Probes: every amide site
Related publication:
PMID 24191053
Experiment details: "Unfolded MBP, initially fully deuterated at exchangeable hydrogen sites in D2O, was allowed to fold for some predetermined time, then probed by a brief pulse of D-to-H labeling to obtain a snapshot of the structure that had been formed to that point. Initial dilution to start folding was into D2O instead of the usual H2O to avoid loss of D during the lengthy (many seconds) prepulse period. For the H-labeling pulse, the refolding protein was diluted by five-fold into H2O buffer at pH 9."
Protection threshold: specific intermediate structure at 7s
Sequence:
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
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EARLY residues
9: I;
10: W;
11: I;
12: N;
13: G;
14: D;
15: K;
16: G;
17: Y;
18: N;
19: G;
20: L;
21: A;
22: E;
23: V;
24: G;
25: K;
26: K;
27: F;
28: E;
29: K;
30: D;
31: T;
32: G;
33: I;
34: K;
35: V;
36: T;
37: V;
38: E;
39: H;
40: P;
41: D;
42: K;
43: L;
60: I;
61: F;
62: W;
260: G;
261: V;
262: L;
263: S;
264: A;
265: G;
266: I;
267: N;
268: A;
269: A;
270: S;
271: P;
272: N;
273: K;
274: E;
275: L;
276: A;
277: K;
278: E;
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INTERMEDIATE
Method: Pulse labeling HDX MS
Conditions: pH 9.0; 20.0 Celsius; Probes: every amide site
Related publication:
PMID 24191053
Experiment details: "Unfolded MBP, initially fully deuterated at exchangeable hydrogen sites in D2O, was allowed to fold for some predetermined time, then probed by a brief pulse of D-to-H labeling to obtain a snapshot of the structure that had been formed to that point. Initial dilution to start folding was into D2O instead of the usual H2O to avoid loss of D during the lengthy (many seconds) prepulse period. For the H-labeling pulse, the refolding protein was diluted by five-fold into H2O buffer at pH 9."
Protection threshold: second foldon unit (60-120s)
Sequence:
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
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INTERMEDIATE residues
78: E;
79: I;
80: T;
81: P;
82: D;
83: K;
84: A;
85: F;
86: Q;
87: D;
88: K;
89: L;
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STRONG
Method: Native exchange NMR
Conditions: pH 7.0; 37.0 Celsius; Probes: 180
Related publication:
PMID 23046344
Experiment details: "Hydrogen exchange NMR experiments were performed in the absence or presence of guanidine hydrochloride (0.2, 0.3, 0.4, 0.6, and 0.8 M) to stay below the unfolding concentration. The protein samples were lyophilized before being dissolved in D2O. The samples were then loaded on a pretuned and preshimmed NMR spectrometer, and the HSQC spectra were recorded at different time intervals using the same acquisition parameters as described above."
Protection threshold: log(P) > 8
Sequence:
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
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STRONG residues
8: V;
9: I;
10: W;
97: V;
106: Y;
114: S;
116: I;
117: Y;
118: N;
124: N;
129: W;
149: F;
157: T;
160: L;
163: A;
193: T;
205: N;
224: M;
225: T;
227: N;
250: F;
263: S;
265: G;
266: I;
279: F;
281: E;
283: Y;
286: T;
329: I;
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MEDIUM
Method: Native exchange NMR
Conditions: pH 7.0; 37.0 Celsius; Probes: 180
Related publication:
PMID 23046344
Experiment details: "Hydrogen exchange NMR experiments were performed in the absence or presence of guanidine hydrochloride (0.2, 0.3, 0.4, 0.6, and 0.8 M) to stay below the unfolding concentration. The protein samples were lyophilized before being dissolved in D2O. The samples were then loaded on a pretuned and preshimmed NMR spectrometer, and the HSQC spectra were recorded at different time intervals using the same acquisition parameters as described above."
Protection threshold: 5 < log(P) < 8
Sequence:
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
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MEDIUM residues
24: G;
25: K;
26: K;
33: I;
35: V;
36: T;
38: E;
53: T;
60: I;
61: F;
62: W;
71: A;
72: Q;
73: S;
77: A;
93: T;
94: W;
95: D;
99: Y;
108: I;
111: E;
112: A;
113: L;
122: L;
136: D;
139: L;
152: Q;
153: E;
156: F;
158: W;
162: A;
169: F;
170: K;
181: V;
183: V;
189: K;
191: G;
194: F;
195: L;
196: V;
206: A;
212: I;
220: G;
222: T;
223: A;
228: G;
241: N;
243: G;
245: T;
249: T;
253: Q;
256: K;
258: F;
260: G;
262: L;
268: A;
282: N;
289: G;
293: V;
294: N;
295: K;
301: A;
304: L;
305: K;
317: I;
320: T;
323: N;
325: Q;
327: G;
330: M;
333: I;
340: W;
342: A;
346: A;
347: V;
349: N;
351: A;
365: Q;
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