Protein Folding Database: Measurement Report

Folding Data

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Note: A field with its data listed as "ND" denotes there is no data for that field.

[Measurement ID: 20] contact us to make corrections & updates to this data

Protein Data
Protein Name	Ribosomal protein L9 N-domain (NTL9)
Oligomeric State	Monomer
Folding Mechanism	Not characterised
Intermediates	0
Phi Pattern	No phi value analysis
SCOP Class	Alpha+Beta \| goto SCOP
SCOP Family	Ribosomal protein L9 N-domain \| goto SCOP

Construct Data
Species	Bacillus stearothermophilus (Bacillus stearothermophilus)	goto 3D view
Sequence	MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQ KQKEQR Blast PFD \| Blast NCBI NR
Length	56
Molecular Weight	6201.28Da
Fusion	None
PDB ID	1DIV \| goto PDB
PDB Resolution	2.6Å
Chain	Any chain
Residues	1 - 56
SCOP ID	55661 \| goto SCOP
UniProt ID	RL9_BACST \| goto UniProt
Relative Contact Order	12.32

Publication Data
Publication	Maxwell KL et al (2005) Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins., Protein Science 14, 602-616 goto pubmed
Data type in publication	Equilibrium & Kinetic \| view other data in this publication

Graphical Analysis Data

Chevron Plot

unfolding & refolding data

ln(k_uH₂O) (s^-1)	ln(k_fH₂O) (s^-1)	m_‡-N (kJ mol^-1 M^-1)	m_‡-D (kJ mol^-1 M^-1)
0.08 ± 0.13	6.55 ± 0.02	0.71 ± 0.04	-1.84 ± 0.04

Notes on Chevron Plot Calculating

Contact Order Plot Data

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Note: Mutant measurements do not have their data plotted on this graph, instead the data from wildtype is marked in red.

view notes on contact order

Equilibrium Data & Methods

Equilibrium Data

[Denaturant] Minimum (M)	[Denaturant] 50% (M)	m_D-N (m) (kJ mol^-1 M^-1)	∆G_D-N (m) (kJ mol^-1)
ND	ND	-2.6	17.3 ± 0.2

Probe

15N -1H chemical shifts (ppm) what is this?

Pertubation

Atomic Force Microscopy what is this?

Technique

Urea

Instrument

750 MHz Bruker DMX Spectrometer

Temperature

Buffer

0.02M TrisHCl

Additive 1:

0.0010M NaCl

Protein Concentration

Kinetic Data & Methods

Kinetic Unfolding Data

[Denaturant] Minimum (M)	[Denaturant] Maximum (M)	k_u (s^-1)	lnk_u (s^-1)	m_u (M^-1)	m_‡-N (kJ mol^-1 M^-1)
7.28	9.46	1.0833 ± 0.0092 (0M)	0.08 ± 0.13 (0M)	ND	0.71 ± 0.04

Kinetic Folding Data

[Denaturant] Minimum (M)	[Denaturant] Maximum (M)	k_fH₂O (s^-1)	ln(k_fH₂O) (s^-1)	m_f (M^-1)	m_‡-D (kJ mol^-1 M^-1)
0.83	9.46	699.24 ± 0.14	6.55 ± 0.02	ND	-1.84 ± 0.04

Probe

Trp Fluorescence what is this?

Pertubation

Denaturant what is this?

Technique

Urea

Instrument

Applied Photophysics SX.18MV Stopped-flow fluorimeter

Temperature

298K

Buffer

0.02M TrisHCl

Additive 1:

0.0010M NaCl

Protein Concentration

Unfolding Fit

Linear

Refolding Fit

Linear

Notes & Comments on this measurement
Measurement Notes
Protein Notes
Construct Notes	PDB entry 1DIV is N and C domains residues 1-149. Contact order is calculated for residues 1-56 only.
Equilibrium Notes	NTL9. Maxwell et al, 2005: The protein was expressed and purified as described (Sato et al., 2001) and characterization under the conditions reported as described (Kuhlman et al., 1998; Sato and Raleigh, 2002; Sato, 2002). The chevron plot represents the faster of two phases. Previous reports indicate that the slower phase reflects proline isomerism (Sato & Raleigh, 2002; Sato, 2002). Sato and Raleigh 2002: Fluorescence detected and CD-detected stopped-flow experiments were performed using an Applied Photophysics SX18MV stopped-flow reaction analyzer, and an AVIV stopped-flow CD spectrometer model 202SF respectively. Fluorescence signals were measured with an excitation wavelength of 276 (±2) nm using a 305 nm cutoff filter. The CD signal at 222 nm was monitored during the reactions. For denaturation jump experiments, protein samples were denatured in a high concentration of denaturant and folding was initiated by an 11-fold dilution into lower concentrations of denaturant. Unfolding was initiated by an 11-fold dilution into higher concentrations of denaturant. The resulting curves were fit with a double-exponential function to obtain first-order rate constants for each phase.
Kinetic Notes	NTL9. Maxwell et al, 2005: The protein was expressed and purified as described (Sato et al., 2001) and characterization under the conditions reported as described (Kuhlman et al., 1998; Sato and Raleigh, 2002; Sato, 2002). The chevron plot represents the faster of two phases. Previous reports indicate that the slower phase reflects proline isomerism (Sato & Raleigh, 2002; Sato, 2002). Sato and Raleigh 2002: Fluorescence detected and CD-detected stopped-flow experiments were performed using an Applied Photophysics SX18MV stopped-flow reaction analyzer, and an AVIV stopped-flow CD spectrometer model 202SF respectively. Fluorescence signals were measured with an excitation wavelength of 276 (±2) nm using a 305 nm cutoff filter. The CD signal at 222 nm was monitored during the reactions. For denaturation jump experiments, protein samples were denatured in a high concentration of denaturant and folding was initiated by an 11-fold dilution into lower concentrations of denaturant. Unfolding was initiated by an 11-fold dilution into higher concentrations of denaturant. The resulting curves were fit with a double-exponential function to obtain first-order rate constants for each phase.
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