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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIC TORD CHAPERONE FROM SHEWANELLA MASSILIA
 
Authors :  S. Tranier, C. Iobbi-Nivol, I. Mortier-Barriere, C. Birck, V. Mejean, J. -P. Samama
Date :  17 Oct 02  (Deposition) - 13 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Tord, 3D-Domain Swapping (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tranier, C. Iobbi-Nivol, C. Birck, M. Ilbert, I. Mortier-Barriere, V. Mejean, J. P. Samama
A Novel Protein Fold And Extreme Domain Swapping In The Dimeric Tord Chaperone From Shewanella Massilia
Structure V. 11 165 2003
PubMed-ID: 12575936  |  Reference-DOI: 10.1016/S0969-2126(03)00008-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TORA SPECIFIC CHAPERONE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21-DE3-PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TORD
    Mutation: YES
    Organism Scientific: SHEWANELLA MASSILIA
    Organism Taxid: 76854

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:41 , GLU A:202 , ALA A:206BINDING SITE FOR RESIDUE DTT A 801
2AC2SOFTWARELEU B:12 , ARG B:29 , PHE B:41BINDING SITE FOR RESIDUE DTT B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N1C)

(-) Exons   (0, 0)

(no "Exon" information available for 1N1C)

(-) 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:199
 aligned with TORD_SHEMA | O87949 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:207
                                                                                                                                                                                                                                       209 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     | 
           TORD_SHEMA     4 VDINHARALVYQLLSSLFAREVDEQRLKELTSEAAQQFWEQLSLEANFTQSVDKIRSTLNGIKDDEALLELAADYCGLFLVGTKHSASPYASLYLSGEDEPLLFGEQHQQMSEFLHQSKLQVQSHFPEPADHLAVMLAYMAHLFCHSENSVQLSFLQTCFNSWLAKFINHLTQCNKNGFYSAVATLTLAWVKQDIAQLEPAVAIIS-   -
               SCOP domains d1n1ca_ A: TorA specific chaperone TorD                                                                                                                                                                         SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------1n1cA02 A:129-210  [code=1.20.1280.20, no name defined]                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...--....hhhhhh------..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n1c A   4 VDINPARALVYQLLSSLFAREVDEQRLKELTSEAAQQFWEQLSLEANFTQSVDKIRSTLNGIKDDEALLELAADYCGLFLVGT--SASPYASLYL------LLFGEQHQQmSEFLHQSKLQVQSHFPEPADHLAVmLAYmAHLCCHSENSVQLSFLQTCVNSWLAKFINHLTQCNKNGFYSAVATLTLAWVKQDIAQLEPAVAIISL 210
                                    13        23        33        43        53        63        73        83  |  |  93    |    - |     113|      123       133     | 143       153       163       173       183       193       203       
                                                                                                             86 89       98    105      114-MSE                  139-MSE                                                                   
                                                                                                                                                                     143-MSE                                                               


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with TORD_SHEMA | O87949 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:210
                                                                                                                                                                                                                                      209     
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    |    -
           TORD_SHEMA     5 DINHARALVYQLLSSLFAREVDEQRLKELTSEAAQQFWEQLSLEANFTQSVDKIRSTLNGIKDDEALLELAADYCGLFLVGTKHSASPYASLYLSGEDEPLLFGEQHQQMSEFLHQSKLQVQSHFPEPADHLAVMLAYMAHLFCHSENSVQLSFLQTCFNSWLAKFINHLTQCNKNGFYSAVATLTLAWVKQDIAQLEPAVAIIS-----   -
               SCOP domains d1n1cb_ B: TorA specific chaperone TorD                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------1n1cB02 B:129-214  [code=1.20.1280.20, no name defined]                                CATH domains
           Pfam domains (1) -----------------------------------Nitrate_red_del-1n1cB01 B:40-177                                                                                                          ------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Nitrate_red_del-1n1cB02 B:40-177                                                                                                          ------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..---....hhhhh.---------hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n1c B   5 DINPARALVYQLLSSLFAREVDEQRLKELTSEAAQQFWEQLSLEANFTQSVDKIRSTLNGIKDDEALLELAADYCGLFLVG---SASPYASLYL---------GEQHQQmSEFLHQSKLQVQSHFPEPADHLAVmLAYmAHLCCHSENSVQLSFLQTCVNSWLAKFINHLTQCNKNGFYSAVATLTLAWVKQDIAQLEPAVAIISLEHHH 214
                                    14        24        34        44        54        64        74        84|   |   94   |     -   |   114       124       134    |  144       154       164       174       184       194       204       214
                                                                                                           85  89       98       108     |                      139-MSE                                                                       
                                                                                                                                       114-MSE                      143-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Nitrate_red_del] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TORD_SHEMA | O87949)
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
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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