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(-) Description

Title :  2OUF-DS, A DISULFIDE-LINKED DIMER OF HELICOBACTER PYLORI PROTEIN HP0242
 
Authors :  N. P. King, M. R. Sawaya, A. W. Jacobitz, T. O. Yeates
Date :  16 Apr 10  (Deposition) - 12 May 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Unknotted Control, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. P. King, A. W. Jacobitz, M. R. Sawaya, L. Goldschmidt, T. O. Yeates
Structure And Folding Of A Designed Knotted Protein.
Proc. Natl. Acad. Sci. Usa V. 107 20732 2010
PubMed-ID: 21068371  |  Reference-DOI: 10.1073/PNAS.1007602107

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HP_0242
    Mutation: YES
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:11 , GLU D:11 , LYS D:17 , ASP D:52BINDING SITE FOR RESIDUE CA D 101
2AC2SOFTWAREGLU A:11 , GLU D:8 , GLU D:11BINDING SITE FOR RESIDUE CA D 102

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:44 -B:44
2C:44 -D:44

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MLI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MLI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MLI)

(-) Exons   (0, 0)

(no "Exon" information available for 3MLI)

(-) Sequences/Alignments

Asymmetric 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:91
 aligned with O25025_HELPY | O25025 from UniProtKB/TrEMBL  Length:94

    Alignment length:91
                                    12        22        32        42        52        62        72        82        92 
          O25025_HELPY    3 DYSELEIFEGNPLDKWNDIIFHASKKLSKKELERLLELLALLETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGN 93
               SCOP domains d3mlia_ A: Hypothetical protein HP0242                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3mli A  3 DYSELEIFEGNPLDKWNDIIFHASKKLSKKELERLLELLALCETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGL 93
                                    12        22        32        42        52        62        72        82        92 


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with O25025_HELPY | O25025 from UniProtKB/TrEMBL  Length:94

    Alignment length:85
                                                                                                            94   
                                    22        32        42        52        62        72        82        92 |   
          O25025_HELPY   13 NPLDKWNDIIFHASKKLSKKELERLLELLALLETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGNE---  -
               SCOP domains d3mlib_ B: Hypothetical protein HP0242                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3mli B 13 NPLDKWNDIIFHASKKLSKKELERLLELLALCETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGLEHHH 97
                                    22        32        42        52        62        72        82        92     


Chain C from PDB  Type:PROTEIN  Length:89
 aligned with O25025_HELPY | O25025 from UniProtKB/TrEMBL  Length:94

    Alignment length:89
                                                                                                              94     
                                    20        30        40        50        60        70        80        90   |     
          O25025_HELPY   11 EGNPLDKWNDIIFHASKKLSKKELERLLELLALLETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGNE-----  -
               SCOP domains d3mlic_ C: Hypothetical protein HP0242                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  3mli C 11 EGNPLDKWNDIIFHASKKLSKKELERLLELLALCETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGLEHHHHH 99
                                    20        30        40        50        60        70        80        90         


Chain D from PDB  Type:PROTEIN  Length:94
 aligned with O25025_HELPY | O25025 from UniProtKB/TrEMBL  Length:94

    Alignment length:94
                                                                                                                      94  
                                    12        22        32        42        52        62        72        82        92 |  
          O25025_HELPY    3 DYSELEIFEGNPLDKWNDIIFHASKKLSKKELERLLELLALLETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGNE--  -
               SCOP domains d3mlid_ D: Hypothetical protein HP0242                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------DUF2018-3mliD01 D:10-92                                                            ---- Pfam domains (1)
           Pfam domains (2) -------DUF2018-3mliD02 D:10-92                                                            ---- Pfam domains (2)
           Pfam domains (3) -------DUF2018-3mliD03 D:10-92                                                            ---- Pfam domains (3)
           Pfam domains (4) -------DUF2018-3mliD04 D:10-92                                                            ---- Pfam domains (4)
         Sec.struct. author hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3mli D  3 DYSELEIFEGNPLDKWNDIIFHASKKLSKKELERLLELLALCETFIEKEDLEEKFESFAKALRIDEELQQKIESRKTDIVIQSMANILSGLEHH 96
                                    12        22        32        42        52        62        72        82        92
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MLI)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF2018] (2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3MLI)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        O25025_HELPY | O25025: 2bo3 3mlg 4u12

(-) Related Entries Specified in the PDB File

2ouf WILD-TYPE PROTEIN
3mlg DESIGNED KNOTTED PROTEIN; A TANDEM DUPLICATION OF HELICOBACTER PYLORI PROTEIN HP0242