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(-) Description

Title :  CRYSTAL STRUCTURE OF METAL-BINDING PROTEIN YODA FROM E. COLI, PFAM DUF149
 
Authors :  S. Eswaramoorthy, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  05 Jul 04  (Deposition) - 20 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Yoda, E. Coli, Structural Genomics, New Fold, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. Swaminathan
Crystal Structure Of A Hypothetical Protein Yoda
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METAL-BINDING PROTEIN YODA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YODA, B1973
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CADMIUM-INDUCED PROTEIN YODA

 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
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:166 , HIS A:175 , HIS A:177 , HOH A:218BINDING SITE FOR RESIDUE ZN A 216

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:125 -A:150

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TXL)

(-) 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:188
 aligned with ZINT_ECOLI | P76344 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:188
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
           ZINT_ECOLI    29 HGKPLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYATDIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGNDSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH 216
               SCOP domains d1txla_ A: Hypothetical protein YodA                                                                                                                                                         SCOP domains
               CATH domains 1txlA00 A:28-215  [code=2.40.128.20, no name defined]                                                                                                                                        CATH domains
               Pfam domains ------YodA-1txlA01 A:34-215                                                                                                                                                                  Pfam domains
         Sec.struct. author .....hhhhhhhhh...hhhhh...hhhhhheeeeehhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhh..eeeeeee..eeeeee..eeeee..eeeeeeeee.....eeeeeeee..........eeeee...........eeeeee..hhhhhhh......eeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txl A  28 HGKPLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYATDIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGNDSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH 215
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
   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, 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 1oek 1s7d 5aq6 5xm5

(-) Related Entries Specified in the PDB File

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