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PDBsum entry 2dcq
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Unknown function PDB id
2dcq

 

 

 

 

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Contents
Protein chain
134 a.a. *
* Residue conservation analysis
PDB id:
2dcq
Name: Unknown function
Title: Fully automated nmr structure determination of the rhodanese homology domain at4g01050(175-295) from arabidopsis thaliana
Structure: Putative protein at4g01050. Chain: a. Fragment: rhodanese hypothetical domain. Synonym: hypothetical protein rafl06-68-j04. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: riken cdna rafl06-68-j04. Expressed in: cell free synthesis. Other_details: e.Coli cell-free protein synthesis
NMR struc: 20 models
Authors: B.Lopez-Mendez,P.Guntert
Key ref: B.López-Méndez and P.Güntert (2006). Automated protein structure determination from NMR spectra. J Am Chem Soc, 128, 13112-13122. PubMed id: 17017791 DOI: 10.1021/ja061136l
Date:
12-Jan-06     Release date:   17-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q9M158  (STR4_ARATH) -  Rhodanese-like domain-containing protein 4, chloroplastic from Arabidopsis thaliana
Seq:
Struc: 		466 a.a.
134 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1021/ja061136l J Am Chem Soc 128:13112-13122 (2006)
PubMed id: 17017791  
 
 
Automated protein structure determination from NMR spectra.
B.López-Méndez, P.Güntert.
 
  ABSTRACT  
 
Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus chemical shift assignments for all (1)H, (13)C, and (15)N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The three-dimensional structures of three 12-16 kDa proteins computed with the FLYA algorithm coincided closely with the conventionally determined structures. Deviations were below 0.95 A for the backbone atom positions, excluding the flexible chain termini. 96-97% of all backbone and side-chain chemical shifts in the structured regions were assigned to the correct residues. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20135044 J.L.Barneto, M.Avalos, R.Babiano, P.Cintas, J.L.Jiménez, and J.C.Palacios (2010).
A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins.
  Org Biomol Chem, 8, 857-863.  
19282963 A.Bahrami, A.H.Assadi, J.L.Markley, and H.R.Eghbalnia (2009).
Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy.
  PLoS Comput Biol, 5, e1000307.  
19722278 B.I.Khayrutdinov, W.J.Bae, Y.M.Yun, J.H.Lee, T.Tsuyama, J.J.Kim, E.Hwang, K.S.Ryu, H.K.Cheong, C.Cheong, J.S.Ko, T.Enomoto, P.A.Karplus, P.Güntert, S.Tada, Y.H.Jeon, and Y.Cho (2009).
Structure of the Cdt1 C-terminal domain: conservation of the winged helix fold in replication licensing factors.
  Protein Sci, 18, 2252-2264.
PDB codes: 2klo 3a4c
  20160991 B.R.Donald, and J.Martin (2009).
Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints.
  Prog Nucl Magn Reson Spectrosc, 55, 101-127.  
20161137 D.C.Rogness, and R.C.Larock (2009).
Rapid synthesis of the indole-indolone scaffold via [3+2] annulation of arynes by methyl indole-2-carboxylates.
  Tetrahedron Lett, 50, 4003-4008.  
19137264 M.P.Williamson, and C.J.Craven (2009).
Automated protein structure calculation from NMR data.
  J Biomol NMR, 43, 131-143.  
18807026 P.Güntert (2009).
Automated structure determination from NMR spectra.
  Eur Biophys J, 38, 129-143.  
19605565 P.Salah, M.Bisaglia, P.Aliprandi, M.Uzan, C.Sizun, and F.Bontems (2009).
Probing the relationship between Gram-negative and Gram-positive S1 proteins by sequence analysis.
  Nucleic Acids Res, 37, 5578-5588.
PDB codes: 2khi 2khj
20333269 R.Powers (2009).
Advances in Nuclear Magnetic Resonance for Drug Discovery.
  Expert Opin Drug Discov, 4, 1077-1098.  
19034675 R.Schmucki, S.Yokoyama, and P.Güntert (2009).
Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm.
  J Biomol NMR, 43, 97.  
19597942 T.Ikeya, M.Takeda, H.Yoshida, T.Terauchi, J.G.Jee, M.Kainosho, and P.Güntert (2009).
Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.
  J Biomol NMR, 44, 261-272.  
17984079 E.L.Ulrich, H.Akutsu, J.F.Doreleijers, Y.Harano, Y.E.Ioannidis, J.Lin, M.Livny, S.Mading, D.Maziuk, Z.Miller, E.Nakatani, C.F.Schulte, D.E.Tolmie, R.Kent Wenger, H.Yao, and J.L.Markley (2008).
BioMagResBank.
  Nucleic Acids Res, 36, D402-D408.  
18761469 J.Shin, W.Lee, and W.Lee (2008).
Structural proteomics by NMR spectroscopy.
  Expert Rev Proteomics, 5, 589-601.  
19021763 M.Takeda, N.Sugimori, T.Torizawa, T.Terauchi, A.M.Ono, H.Yagi, Y.Yamaguchi, K.Kato, T.Ikeya, J.Jee, P.Güntert, D.J.Aceti, J.L.Markley, and M.Kainosho (2008).
Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR.
  FEBS J, 275, 5873-5884.
PDB code: 2jz4
18818721 P.R.Markwick, T.Malliavin, and M.Nilges (2008).
Structural biology by NMR: structure, dynamics, and interactions.
  PLoS Comput Biol, 4, e1000168.  
17451164 J.R.Baker, D.N.Woolfson, F.W.Muskett, R.G.Stoneman, M.D.Urbaniak, and S.Caddick (2007).
Protein-small molecule interactions in neocarzinostatin, the prototypical enediyne chromoprotein antibiotic.
  Chembiochem, 8, 704-717.  
17221977 J.Zhao, and R.C.Larock (2007).
Synthesis of xanthones, thioxanthones, and acridones by the coupling of arynes and substituted benzoates.
  J Org Chem, 72, 583-588.  
18007625 M.Takeda, T.Ikeya, P.Güntert, and M.Kainosho (2007).
Automated structure determination of proteins with the SAIL-FLYA NMR method.
  Nat Protoc, 2, 2896-2902.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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