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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF NP24-I, A THAUMATIN-LIKE PROTEIN
 
Authors :  C. Chakrabarti, R. Ghosh
Date :  11 Aug 06  (Deposition) - 24 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Protein, Antifungal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ghosh, C. Chakrabarti
Crystal Structure Analysis Of Np24-I: A Thaumatin-Like Protein
Planta V. 228 883 2008
PubMed-ID: 18651170  |  Reference-DOI: 10.1007/S00425-008-0790-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN NP24
    Chains: A
    Organism Scientific: SOLANUM LYCOPERSICUM
    Organism Taxid: 4081
    Other Details: RIPE TOMATO
    Synonym: PATHOGENESIS-RELATED PROTEIN PR P23, SALT-INDUCED PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:35 , PRO A:37 , ARG A:200 , HOH A:247BINDING SITE FOR RESIDUE CL A 208

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:204
2A:51 -A:61
3A:66 -A:72
4A:120 -A:192
5A:125 -A:175
6A:133 -A:143
7A:147 -A:156
8A:157 -A:162

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:18 -Pro A:19
2Pro A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_NP24_SOLLC_001 *I24FNP24_SOLLC  ---  ---AI3F
2UniProtVAR_NP24_SOLLC_002 *S38FNP24_SOLLC  ---  ---AS17F
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THAUMATIN_1PS00316 Thaumatin family signature.NP24_SOLLC78-93  1A:57-72

(-) Exons   (0, 0)

(no "Exon" information available for 2I0W)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:207
 aligned with NP24_SOLLC | P12670 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:207
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
           NP24_SOLLC    22 ATIEVRNNCPYTVWAASTPIGGGRRLNRGQTWVINAPRGTKMARIWGRTGCNFNAAGRGTCQTGDCGGVLQCTGWGKPPNTLAEYALDQFSNLDFWDISLVDGFNIPMTFAPTKPSGGKCHAIHCTANINGECPRALKVPGGCNNPCTTFGGQQYCCTQGPCGPTELSKFFKKRCPDAYSYPQDDPTSTFTCPGGSTNYRVVFCPNG 228
               SCOP domains d2i0wa_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 2i0wA00 A:1-207 Thaumatin                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee...eeeee....eeeee.......eeeeee...eee...eee.....................eeeeeee....eeeeeee........eeeee..........eee..hhhhhh....ee..ee.hhhhhh.hhhhhh.........hhhhhhhhh..............eeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) --F-------------F---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------THAUMATIN_1     --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i0w A   1 ATIEVRNNCPYTVWAASTPIGGGRRLNRGQTWVINAPRGTKMARIWGRTGCNFNAAGRGTCQTGDCGGVLQCTGWGKPPNTLAEYALDQFSNLDFWDISLVDGFNIPMTFAPTKPSGGKCHAIHCTANINGECPRALKVPGGCNNPCTTFGGQQYCCTQGPCGPTELSKFFKKRCPDAYSYPQDDPTSTFTCPGGSTNYRVVFCPNG 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I0W)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NP24_SOLLC | P12670)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    GO:0009607    response to biotic stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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