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(-) Description

Title :  YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH ZINC IONS
 
Authors :  G. David, K. Blondeau, M. Renouard, S. Penel, A. Lewit-Bentley
Date :  28 Mar 03  (Deposition) - 15 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Stress Protein/Lipocalin, Stress Protein, Lipocalin, Yoda (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. David, K. Blondeau, M. Schiltz, S. Penel, A. Lewit-Bentley
Yoda From Escherichia Coli Is A Metal-Binding, Lipocalin-Like Protein
J. Biol. Chem. V. 278 43728 2003
PubMed-ID: 12909634  |  Reference-DOI: 10.1074/JBC.M304484200

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YODA
    Chains: A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:144 , HIS A:155 , HOH A:2023 , HOH A:2025BINDING SITE FOR RESIDUE ZN A1194
2AC2SOFTWAREHIS A:153 , TYR A:177 , GLU A:189 , HIS A:193BINDING SITE FOR RESIDUE ZN A1195
3AC3SOFTWAREGLU A:93 , HIS A:95 , HOH A:2026BINDING SITE FOR RESIDUE ZN A1196
4AC4SOFTWAREASP A:24 , GLN A:47 , HIS A:75 , HOH A:2027 , HOH A:2028BINDING SITE FOR RESIDUE ZN A1197

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:103 -A:128

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OEK)

(-) 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:185
 aligned with ZINT_ECOLI | P76344 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:185
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           ZINT_ECOLI    32 PLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYATDIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGNDSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH 216
               SCOP domains d1oeka_ A: Hypothetical protein YodA                                                                                                                                                      SCOP domains
               CATH domains 1oekA00 A:9-193  [code=2.40.128.20, no name defined]                                                                                                                                      CATH domains
               Pfam domains ---YodA-1oekA01 A:12-193                                                                                                                                                                  Pfam domains
         Sec.struct. author ..hhhhhhhhh...hhhhh...hhhhh.eeeeehhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee..eeeee....eeeee.eeeeeeeee.....eeeeeeee..........eeeee...........eeeeee..hhhhhhhh.....eeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oek A   9 PLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYATDIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGNDSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH 193
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ZINT_ECOLI | P76344)
molecular function
    GO:0046870    cadmium ion binding    Interacting selectively and non-covalently with cadmium (Cd) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0034224    cellular response to zinc ion starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of zinc ions.
    GO:0046686    response to cadmium ion    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 cadmium (Cd) ion stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        ZINT_ECOLI | P76344: 1oee 1oej 1s7d 1txl 5aq6 5xm5

(-) Related Entries Specified in the PDB File

1oee YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH CADMIUM IONS
1oej YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH NO ADDED IONS