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(-) Description

Title :  FULLY AUTOMATED NMR STRUCTURE DETERMINATION OF THE RHODANESE HOMOLOGY DOMAIN AT4G01050(175-295) FROM ARABIDOPSIS THALIANA
 
Authors :  B. Lopez-Mendez, P. Guntert
Date :  12 Jan 06  (Deposition) - 17 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rhodanese Domain, Fully Automated Structure Determination, Flya Algorithm, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Lopez-Mendez, P. Guntert
Automated Protein Structure Determination From Nmr Spectra
J. Am. Chem. Soc. V. 128 13112 2006
PubMed-ID: 17017791  |  Reference-DOI: 10.1021/JA061136L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE PROTEIN AT4G01050
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP030120-27
    Expression System Vector TypePLASMID
    FragmentRHODANESE HYPOTHETICAL DOMAIN
    GeneRIKEN CDNA RAFL06-68-J04
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsE.COLI CELL-FREE PROTEIN SYNTHESIS
    SynonymHYPOTHETICAL PROTEIN RAFL06-68-J04

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DCQ)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DCQ)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:134
 aligned with STR4_ARATH | Q9M158 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:192
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273  
           STR4_ARATH    84 SSFDSDGLIEGISNFVTDNPLVIAGGVAALAVPFVLSQVLNKKPKSWGVESAKNAYTKLGTDDNAQLLDIRATADFRQVGSPNIKGLGKKAVSTVYNGEDKPGFLKKLSLKFKDPENTTLYILDKFDGNSELVAELVALNGFKSAYAIKDGAEGPRGWLNSSLPWIEPKKTLSLDLSSLTDSISGVFGESSD 275
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......-------------------------------------------hhhhhhhhhhhh...eeee....hhhhhh....hhhhh...ee.......hhhhhh.............eeee.....hhhhhhhhhhhh....ee...........hhhhh..........---------------hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dcq A   1 GSSGSSG-------------------------------------------SAKNAYTKLGTDDNAQLLDIRATADFRQVGSPNIKGLGKKAVSTVYNGEDKPGFLKKLSLKFKDPENTTLYILDKFDGNSELVAELVALNGFKSAYAIKDGAEGPRGWLNSSLPWIEPKKTS---------------GPSSG 134
                                  |  -         -         -         -         -|       17        27        37        47        57        67        77        87        97       107       117       127 |       -       132  
                                  7                                           8                                                                                                                      129             130    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2DCQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DCQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DCQ)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (STR4_ARATH | Q9M158)
molecular function
    GO:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0009772    photosynthetic electron transport in photosystem II    A photosynthetic electron transport chain in which electrons move from the primary electron acceptor (Quinone, Q) through a chain of electron transport molecules in the thylakoid membrane until they reach the ultimate electron acceptor of Photosystem II, which is plastocyanin (PC). The electron is then passed to the P700 chlorophyll a molecules of the reaction centre of photosystem I.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009941    chloroplast envelope    The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
    GO:0009534    chloroplast thylakoid    Sac-like membranous structures (cisternae) in a chloroplast combined into stacks (grana) and present singly in the stroma (stroma thylakoids or frets) as interconnections between grana. An example of this component is found in Arabidopsis thaliana.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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 Related Entries

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        STR4_ARATH | Q9M1581vee

(-) Related Entries Specified in the PDB File

1vee STRUCTURE OF THE SAME PROTEIN DETERMINED BY CONVENTIONAL NMR METHODS