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(-) Description

Title :  CRYSTAL STRUCTURE OF REFINED TETRAGONAL CRYSTAL OF YODA FROM ESCHERICHIA COLI
 
Authors :  D. H. Shin, H. Yokota, R. Kim, S. H. Kim, Berkeley Structural Genomics (Bsgc)
Date :  29 Jan 04  (Deposition) - 10 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Hypothetical, Structural Genomics, X-Ray Crytsallography, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of Refined Tetragonal Crystal Of Yoda Fro Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:144 , HIS A:155 , HOH A:301 , HOH A:366 , HOH A:368BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS A:153 , GLU A:189 , HIS A:193BINDING SITE FOR RESIDUE ZN A 202
3AC3SOFTWAREGLU A:93 , HIS A:95 , HOH A:379BINDING SITE FOR RESIDUE ZN A 203
4AC4SOFTWAREASP A:24 , HIS A:75 , HOH A:337 , HOH A:380BINDING SITE FOR RESIDUE ZN A 204

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S7D)

(-) Exons   (0, 0)

(no "Exon" information available for 1S7D)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:187
 aligned with ZINT_ECOLI | P76344 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:187
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       
           ZINT_ECOLI    30 GKPLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYATDIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGNDSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH 216
               SCOP domains d1s7da_ A: Hypothetical protein YodA                                                                                                                                                        SCOP domains
               CATH domains 1s7dA00 A:7-193  [code=2.40.128.20, no name defined]                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh....hhhhh...hhhhhheeeeehhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh....eeeee..eeeee....eeeee.eeeeeeeee.....eeeeeeee..........eeeee...........eeeeee..hhhhhhhh.....eeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s7d A   7 GKPLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYATDIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGNDSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH 193
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
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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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S7D)

(-) Gene Ontology  (8, 8)

Asymmetric 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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  1s7d
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 Related Entries

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

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

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