Start2Fold

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

Entry STF0012

French bean apoplastocyanin

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Protein information

Name of the protein: Plastocyanin
Organism: Phaseolus vulgaris (Kidney bean) (French bean)
Number of residues: 99
Related UniProt entry:   P00287 (Fragment: 1 - 99)
Related PDB entry:   9PCY

Visualize the data

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Experiment sets

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EARLY

Method: HDX-folding competition by NMR

Conditions: pH 5.0-5.9; 25.0 Celsius; Probes: 29

Related publication:
 PMID 8241116

Experiment details: "Apo-Pc was first exchanged by repetitive ultrafiltration into D2O buffer containing potassium phosphate (50 mM), NaCl (1 M), 2-mercaptoethanol (l0 mM), and EDTA (0.1 mM) (pH* 7.0, direct meter reading uncorrected for isotope effect). The protein was unfolded in the D2O buffer containing 2.2 M GuHCl and kept at 25C for 1 h. The refolding reaction was initiated by 1:21 dilution in D2O buffer without GuHCl. After a delay of 90 s to allow completion of the faster refolding reactions, the competition experiment was initiated by 1:9 dilution with either potassium phosphate (50 mM, pH 5.9) containing NaCl (1 M), 2-mercaptoethanol (10 mM), and EDTA (0.1 mM) in H2O or sodium acetate (50 mM, pH 5.0) containing NaCl (1.5 M), 2-mercaptoethanol (10 mM), and EDTA (0.1 mM) in H2O. The final pH values were 6.0 and 5.2, respectively."

Protection threshold: P > 20

Sequence: LEVLLGSGDGSLVFVPSEFSVPSGEKIVFKNNAGFPHNVVFDEDEIPAGVDAVKISMPEEELLNAPGETYVVTLDTKGTYSFYCSPHQGAGMVGKVTVN
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EARLY residues

70: Y; 72: V; 80: Y; 82: F; 83: Y; 95: K;
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INTERMEDIATE

Method: HDX-folding competition by NMR

Conditions: pH 5.0-5.9; 25.0 Celsius; Probes: 29

Related publication:
 PMID 8241116

Experiment details: "Apo-Pc was first exchanged by repetitive ultrafiltration into D2O buffer containing potassium phosphate (50 mM), NaCl (1 M), 2-mercaptoethanol (l0 mM), and EDTA (0.1 mM) (pH* 7.0, direct meter reading uncorrected for isotope effect). The protein was unfolded in the D2O buffer containing 2.2 M GuHCl and kept at 25C for 1 h. The refolding reaction was initiated by 1:21 dilution in D2O buffer without GuHCl. After a delay of 90 s to allow completion of the faster refolding reactions, the competition experiment was initiated by 1:9 dilution with either potassium phosphate (50 mM, pH 5.9) containing NaCl (1 M), 2-mercaptoethanol (10 mM), and EDTA (0.1 mM) in H2O or sodium acetate (50 mM, pH 5.0) containing NaCl (1.5 M), 2-mercaptoethanol (10 mM), and EDTA (0.1 mM) in H2O. The final pH values were 6.0 and 5.2, respectively."

Protection threshold: 10 < P < 20

Sequence: LEVLLGSGDGSLVFVPSEFSVPSGEKIVFKNNAGFPHNVVFDEDEIPAGVDAVKISMPEEELLNAPGETYVVTLDTKGTYSFYCSPHQGAGMVGKVTVN
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

INTERMEDIATE residues

4: L; 5: L; 15: V; 21: V; 27: I; 28: V; 98: V;
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LATE

Method: HDX-folding competition by NMR

Conditions: pH 5.0-5.9; 25.0 Celsius; Probes: 29

Related publication:
 PMID 8241116

Experiment details: "Apo-Pc was first exchanged by repetitive ultrafiltration into D2O buffer containing potassium phosphate (50 mM), NaCl (1 M), 2-mercaptoethanol (l0 mM), and EDTA (0.1 mM) (pH* 7.0, direct meter reading uncorrected for isotope effect). The protein was unfolded in the D2O buffer containing 2.2 M GuHCl and kept at 25C for 1 h. The refolding reaction was initiated by 1:21 dilution in D2O buffer without GuHCl. After a delay of 90 s to allow completion of the faster refolding reactions, the competition experiment was initiated by 1:9 dilution with either potassium phosphate (50 mM, pH 5.9) containing NaCl (1 M), 2-mercaptoethanol (10 mM), and EDTA (0.1 mM) in H2O or sodium acetate (50 mM, pH 5.0) containing NaCl (1.5 M), 2-mercaptoethanol (10 mM), and EDTA (0.1 mM) in H2O. The final pH values were 6.0 and 5.2, respectively."

Protection threshold: 4 < P < 10

Sequence: LEVLLGSGDGSLVFVPSEFSVPSGEKIVFKNNAGFPHNVVFDEDEIPAGVDAVKISMPEEELLNAPGETYVVTLDTKGTYSFYCSPHQGAGMVGKVTVN
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LATE residues

3: V; 40: V; 96: V;
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STRONG

Method: Native exchange NMR

Conditions: pH 7.0; 20.0 Celsius; Probes: all

Related publication:
 PMID 3172230

Experiment details: "Very slowly exchanging amide protons were identified on the basis of observation of backbone NH/CH peaks in 2QF-COSY or 2Q spectra acquired 3.5 months after exchange into D2O at pH 7.0."

Protection threshold: very slowly exchanging amid protons

Sequence: LEVLLGSGDGSLVFVPSEFSVPSGEKIVFKNNAGFPHNVVFDEDEIPAGVDAVKISMPEEELLNAPGETYVVTLDTKGTYSFYCSPHQGAGMVGKVTVN
 CLICK TO DOWNLOAD SEQUENCE IN FASTA

STRONG residues

3: V; 4: L; 5: L; 13: V; 14: F; 15: V; 21: V; 27: I; 28: V; 29: F; 30: K; 37: H; 38: N; 39: V; 40: V; 41: F; 70: Y; 72: V; 78: G; 80: Y; 82: F; 83: Y; 84: C; 94: G; 95: K; 96: V; 97: T; 98: V;
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