Start2Fold

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

Entry STF0056

cellular retinol-binding protein type-1

 DOWNLOAD ENTRY IN XML

Protein information

Name of the protein: Retinol-binding protein 1
Organism: Rattus norvegicus (Rat)
Number of residues: 134
Related UniProt entry:   P02696 (Fragment: 1 - 135)
Related PDB entry:   1JBH

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

STRONG

Method: Native exchange NMR

Conditions: pH 6.0; 25.0 Celsius; Probes: 124

Related publication:
 PMID 19965581

Experiment details: "For the identification of slow exchanging amide protons, the protein sample buffer was replaced with a perdeuterated solution consisting of 20 mM KD2PO4 and 0.05% NaN3 in D2O, as previously described (36). This perdeuterated solution was prepared from the protonated buffer (90% H2O/10% D2O) at pH 6.0 by lyophilizing and redissolving in D2O twice. The buffer exchange was performed at 4°C with Vivaspin centrifugal concentrators (molecular weight cutoff of 10 kDa) in several rounds of filtration over 6–10 h. Following equilibration to 25°C inside the NMR magnet, a series of homonuclear TOCSY (alternating beween 30 and 80 ms spin lock time) and NOESY (alternating between 80 and 150 ms mixing time) experiments were collected over a period of more than 9 days (the first 3.5 days at 600.13 MHz and the remaining time at 499.87 MHz) in order to monitor the amide proton exchange."

Protection threshold: no exchange for >220 hours

Sequence: MPVDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDDRKCMTTVSWDGDKLQCVQKGEKEGRGWTQWIEGDELHLEMRAEGVTCKQVFKKVH
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

7: G; 9: W; 10: K; 12: L; 20: Y; 21: L; 22: R; 23: A; 24: L; 41: K; 42: E; 43: I; 44: V; 50: M; 51: I; 52: I; 53: R; 65: F; 71: F; 85: T; 88: S; 93: K; 95: Q; 96: C; 107: W; 108: T; 109: Q; 110: W; 112: E; 116: L; 117: H; 118: L; 119: E; 120: M; 121: R; 122: A; 125: V; 127: C; 129: Q; 130: V; 131: F; 132: K;
 CLICK TO DOWNLOAD LIST OF RESIDUES

 Show  Hide

MEDIUM

Method: Native exchange NMR

Conditions: pH 6.0; 25.0 Celsius; Probes: 124

Related publication:
 PMID 19965581

Experiment details: "For the identification of slow exchanging amide protons, the protein sample buffer was replaced with a perdeuterated solution consisting of 20 mM KD2PO4 and 0.05% NaN3 in D2O, as previously described (36). This perdeuterated solution was prepared from the protonated buffer (90% H2O/10% D2O) at pH 6.0 by lyophilizing and redissolving in D2O twice. The buffer exchange was performed at 4°C with Vivaspin centrifugal concentrators (molecular weight cutoff of 10 kDa) in several rounds of filtration over 6–10 h. Following equilibration to 25°C inside the NMR magnet, a series of homonuclear TOCSY (alternating beween 30 and 80 ms spin lock time) and NOESY (alternating between 80 and 150 ms mixing time) experiments were collected over a period of more than 9 days (the first 3.5 days at 600.13 MHz and the remaining time at 499.87 MHz) in order to monitor the amide proton exchange."

Protection threshold: no exchange for >20 hours

Sequence: MPVDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDDRKCMTTVSWDGDKLQCVQKGEKEGRGWTQWIEGDELHLEMRAEGVTCKQVFKKVH
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

MEDIUM residues

13: S; 25: D; 40: D; 83: C; 86: T; 87: V; 97: V; 111: I; 115: E; 128: K;
 CLICK TO DOWNLOAD LIST OF RESIDUES