Entry STF0004
Sperm whale apo-myoglobin
Protein information
Name of the protein: | Myoglobin |
Organism: | Physeter macrocephalus |
Number of residues: | 153 |
Related UniProt entry: | P02185 (Fragment: 2 - 154) |
Related PDB entry: | 1MBC |
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: Pulse labeling HDX NMR
Conditions: pH 5.8; 25.0 Celsius; Probes: 51
Related publication:
PMID 18779573
Experiment details: "A solution containing the fully unfolded apo-myoglobin (80 M) at pH 2.2 in HCl/H2O was placed in syringe P. Refolding and H/D exchange was performed at room temperature. The refolding reaction was initiated by a 6-fold dilution of the acid-unfolded apo-myoglobin with either 60 mM acetate buffer or 30 mM citrate buffer in D2O delivered from syringe Q, to a final (uncorrected) pH of 5.8. After refolding times (tf) of 0.4 or 6 ms, the H/D exchange reaction was initiated by a 1/6-fold dilution of the sample solution with D2O buffer containing 350-mM 3-(cyclohexylamino)-1 propanesulfonic acid (CAPS) delivered from syringe R at the desired pH* from 7 to 10.7 to enhance exchange of unprotected amide protons to deuterons. The H/D exchange labeling was allowed to proceed for 3.6 ms."
Protection threshold: k(cl)/k(op) > 80
Sequence:
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
CLICK TO DOWNLOAD SEQUENCE IN FASTA
EARLY residues
10: V;
11: L;
14: W;
30: I;
107: I;
110: A;
111: I;
112: I;
113: H;
114: V;
115: L;
138: F;
CLICK TO DOWNLOAD LIST OF RESIDUES
INTERMEDIATE
Method: Pulse labeling HDX NMR
Conditions: pH 5.8; 25.0 Celsius; Probes: 51
Related publication:
PMID 18779573
Experiment details: "A solution containing the fully unfolded apo-myoglobin (80 M) at pH 2.2 in HCl/H2O was placed in syringe P. Refolding and H/D exchange was performed at room temperature. The refolding reaction was initiated by a 6-fold dilution of the acid-unfolded apo-myoglobin with either 60 mM acetate buffer or 30 mM citrate buffer in D2O delivered from syringe Q, to a final (uncorrected) pH of 5.8. After refolding times (tf) of 0.4 or 6 ms, the H/D exchange reaction was initiated by a 1/6-fold dilution of the sample solution with D2O buffer containing 350-mM 3-(cyclohexylamino)-1 propanesulfonic acid (CAPS) delivered from syringe R at the desired pH* from 7 to 10.7 to enhance exchange of unprotected amide protons to deuterons. The H/D exchange labeling was allowed to proceed for 3.6 ms."
Protection threshold: 50 < k(cl)/k(op) < 80
Sequence:
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
CLICK TO DOWNLOAD SEQUENCE IN FASTA
INTERMEDIATE residues
9: L;
17: V;
109: E;
134: A;
139: R;
CLICK TO DOWNLOAD LIST OF RESIDUES
LATE
Method: Pulse labeling HDX NMR
Conditions: pH 5.8; 25.0 Celsius; Probes: 51
Related publication:
PMID 18779573
Experiment details: "A solution containing the fully unfolded apo-myoglobin (80 M) at pH 2.2 in HCl/H2O was placed in syringe P. Refolding and H/D exchange was performed at room temperature. The refolding reaction was initiated by a 6-fold dilution of the acid-unfolded apo-myoglobin with either 60 mM acetate buffer or 30 mM citrate buffer in D2O delivered from syringe Q, to a final (uncorrected) pH of 5.8. After refolding times (tf) of 0.4 or 6 ms, the H/D exchange reaction was initiated by a 1/6-fold dilution of the sample solution with D2O buffer containing 350-mM 3-(cyclohexylamino)-1 propanesulfonic acid (CAPS) delivered from syringe R at the desired pH* from 7 to 10.7 to enhance exchange of unprotected amide protons to deuterons. The H/D exchange labeling was allowed to proceed for 3.6 ms."
Protection threshold: 20 < k(cl)/k(op) < 50
Sequence:
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
CLICK TO DOWNLOAD SEQUENCE IN FASTA
LATE residues
29: L;
31: R;
32: L;
33: F;
104: L;
106: F;
135: L;
CLICK TO DOWNLOAD LIST OF RESIDUES
STRONG
Method: Native exchange NMR
Conditions: pH 6.0; 5.0 Celsius; Probes: every amide site
Related publication:
PMID 2218495
Experiment details: "Apo-Mb in H2O solution was diluted into buffered D2O, initiating H/D exchange. After a period of "exchange-out," further exchange was quenched by the addition of heme and adjusting the pH, and exchange was evaluated by 2D H NMR."
Protection threshold: P > 50000
Sequence:
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
CLICK TO DOWNLOAD SEQUENCE IN FASTA
STRONG residues
10: V;
11: L;
14: W;
17: V;
30: I;
112: I;
114: V;
115: L;
CLICK TO DOWNLOAD LIST OF RESIDUES
MEDIUM
Method: Native exchange NMR
Conditions: pH 6.0; 5.0 Celsius; Probes: every amide site
Related publication:
PMID 2218495
Experiment details: "Apo-Mb in H2O solution was diluted into buffered D2O, initiating H/D exchange. After a period of "exchange-out," further exchange was quenched by the addition of heme and adjusting the pH, and exchange was evaluated by 2D H NMR."
Protection threshold: 5000 < P < 50000
Sequence:
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
CLICK TO DOWNLOAD SEQUENCE IN FASTA
MEDIUM residues
9: L;
18: E;
29: L;
31: R;
33: F;
40: L;
69: L;
110: A;
133: K;
138: F;
CLICK TO DOWNLOAD LIST OF RESIDUES
STRONG
Method: Native exchange in partially folded state by NMR
Conditions: pH 4.2; 5.0 Celsius; Probes: every amide site
Related publication:
PMID 2218495
Experiment details: "Apo-Mb in H2O solution was diluted into buffered D2O, initiating H/D exchange. After a period of "exchange-out," further exchange was quenched by the addition of heme and adjusting the pH, and exchange was evaluated by 2D H NMR."
Protection threshold: P > 30
Sequence:
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
CLICK TO DOWNLOAD SEQUENCE IN FASTA
STRONG residues
9: L;
10: V;
11: L;
17: V;
107: I;
112: I;
114: V;
142: I;
CLICK TO DOWNLOAD LIST OF RESIDUES
MEDIUM
Method: Native exchange in partially folded state by NMR
Conditions: pH 4.2; 5.0 Celsius; Probes: every amide site
Related publication:
PMID 2218495
Experiment details: "Apo-Mb in H2O solution was diluted into buffered D2O, initiating H/D exchange. After a period of "exchange-out," further exchange was quenched by the addition of heme and adjusting the pH, and exchange was evaluated by 2D H NMR."
Protection threshold: 10 < P < 30
Sequence:
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
CLICK TO DOWNLOAD SEQUENCE IN FASTA
MEDIUM residues
14: W;
18: E;
30: I;
138: F;
143: A;
CLICK TO DOWNLOAD LIST OF RESIDUES