The Protein Folding Database
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  Statistics
Version: 2.2
Last Update: 8-Jun-2007
Entries: 296
Proteins: 70
Families: 53
Species: 30
ϕ values: 230 (5 proteins)
Locations of visitors to this page
  Latest Additions
ACBP (3 WT)
FRB (6 WT)
CI2 (3 WT, 202 mutants)
HPr (1 WT, 4 mutants)
Im7 (1 WT)
En-HD (1 WT)
Im9 (2 WT)
Abp1 SH3 (1 WT)
CheW (1 WT)
U1A (1 WT)
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Fulton et al (2005) Nucleic Acids Res. 33:D279-283  |  Fulton et al (2007) Nucleic Acids Res. 35:D304-307 About PFD | Help | Glossary
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: 12] contact us to make corrections & updates to this data

Expand   Protein Data
Protein Name Hypothetical protein YjbJ from Escherichia coli (EC0298)
Oligomeric State Monomer
Folding Mechanism Not characterised
Intermediates 0
Phi Pattern No phi value analysis
SCOP Class Alpha   |   goto SCOP
SCOP Family Hypothetical protein YjbJ   |   goto SCOP

Expand   Construct Data
Species E. coli (Escherichia coli)

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Sequence MGSSHHHHHHSSGLVPRCSHMNKDEAGGNWKQFKGKVKEQWGKLTDDDMT
IIEGKRDQLVGKIQERYGYQKDQAEKEVVDWETRNEYRW

Blast PFD  |  Blast NCBI NR
Length 89
Molecular Weight 10516.6Da
Fusion N-terminal hexahistidine
PDB ID 1RYK   |   goto PDB  
PDB Resolution NMR
Chain Any chain
Residues 1 - 69
SCOP ID 69050   |   goto SCOP
UniProt ID YJBJ_ECOLI   |   goto UniProt
Relative Contact Order 8.65

Expand   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

Expand   Graphical Analysis Data
Contact Order Plot Data Acyl Coenzyme A Binding Protein Hypothetical protein YjbJ from Escherichia coli E colicin binding Immunity Protein 7 (ImmE7*) E colicin binding Immunity Protein 9 (ImmE9) Lambda C1 repressor, DNA-binding domain E colicin binding Immunity Protein 9 (ImmE9) Acyl Coenzyme A Binding Protein Acyl Coenzyme A Binding Protein Internalin B, C-terminal domain Apo-azurin Chemotaxis protein CheW Fyn proto-oncogene tyrosine kinase, SH3 domain Alpha-Spectrin SH3 Domain c-src tyrosine kinase SH3 Domain Actin binding protein 1 SH3 domain Activation Domain Of Human Procarboxypeptidase A2 Chymotrypsin Inhibitor 2 Ribosomal protein L9 C-domain FK-506 binding protein Ribosomal protein L23 Acylphosphatase Ribosomal protein L9 N-domain Immunoglobulin-binding protein G Immunoglobulin light chain-binding domain of protein L c-Raf1 RBD Ribosomal protein S6 c-src tyrosine kinase SH2 domain Spliceosomal U1A protein Ubiquitin FK-506 binding protein Chymotrypsin Inhibitor 2 Chymotrypsin Inhibitor 2
generated contact order graph

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To view more data on a SCOP Class click on it's name in the legend.
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

Expand   Equilibrium Data & Methods
Equilibrium Data
[Denaturant] Minimum
(M)		 [Denaturant] 50%
(M)		 mD-N (m)
(kJ mol-1 M-1)		 ∆GD-N (m)
(kJ mol-1)
ND ND -14.1 ± 1.9 11.4 ± 1.6
Probe Far-UV Circular Dichroism  what is this?
Pertubation Temperature  what is this?
Technique Temperature
Instrument Standard Circular Dichroism Spectrometer  what is this?
Temperature 298K
pH 7
Buffer 0.05M Phosphate
Protein Concentration ND

Expand   Kinetic Data & Methods
Kinetic Unfolding Data
[Denaturant] Minimum
(M)		 [Denaturant] Maximum
(M)		 ku
(s-1)		 lnku
(s-1)		 mu
(M-1)		 m‡-N
(kJ mol-1 M-1)
ND ND 89.12 ± 17.1 (0M) 4.49 ± 0.61 (0M) ND 5.95 ± 0.37
Kinetic Folding Data
[Denaturant] Minimum
(M)		 [Denaturant] Maximum
(M)		 kfH2O
(s-1)		 ln(kfH2O)
(s-1)		 mf
(M-1)		 m‡-D
(kJ mol-1 M-1)
ND ND 8777.97 ± 63.28 9.08 ± 0.12 ND -8.16 ± 0.27
Probe Trp Fluorescence  what is this?
Pertubation Temperature  what is this?
Technique Temperature
Instrument Standard Stopped-Flow Spectrophotometer  what is this?
Temperature 298K
pH 7
Buffer 0.05M Phosphate
Protein Concentration ND
Unfolding Fit Linear
Refolding Fit Linear

Expand   Notes & Comments on this measurement
Measurement Notes
Protein Notes 5 helices; bundle of two orthogonally packed alpha-hairpins; involved in the interactions with DNA and proteins. Structural Genomics, Unknown Function.
Construct Notes Absolute CO was calculated using PDB entry 1RYK. This structure does not contain the N-terminal 20 residues.
Equilibrium Notes EC0298. From Maxwell et al, 2005: The protein was cloned into pet15B (which has a thrombin cleavage site) and expressed and purified as previously described (Maxwell et al., 2003). Folding/unfolding rates were determined under the conditions described by laser T-jump fluorescence spectroscopy (Qiu et al., 2002). Equilibrium free energy was obtained from a GuHCl titration as monitored by CD. As monitored by the coincidence of the kinetically and equilibrium-derived folding free energy, this protein folds via an apparently two-state process. (LQ, DB, KLM, SJH). Qiu, L.L., Pabit, S.A., Roitberg, A.E., and Hagen, S.J. 2002. Smaller and faster: The 20-residue Trp-cage protein folds in 4 micros
Kinetic Notes EC0298. From Maxwell et al, 2005: The protein was cloned into pet15B (which has a thrombin cleavage site) and expressed and purified as previously described (Maxwell et al., 2003). Folding/unfolding rates were determined under the conditions described by laser T-jump fluorescence spectroscopy (Qiu et al., 2002). Equilibrium free energy was obtained from a GuHCl titration as monitored by CD. As monitored by the coincidence of the kinetically and equilibrium-derived folding free energy, this protein folds via an apparently two-state process. (LQ, DB, KLM, SJH). Qiu, L.L., Pabit, S.A., Roitberg, A.E., and Hagen, S.J. 2002. Smaller and faster: The 20-residue Trp-cage protein folds in 4 micros
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