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(-) Description

Title :  STRUCTURE OF THE HYPOTHETICAL PROTEIN YGIW FROM E. COLI.
 
Authors :  C. Lehmann, A. Galkin, S. Pullalarevu, E. Sarikaya, W. Krajewski, K. Lim, A. Howard, O. Herzberg, Structure 2 Function Project (S2F
Date :  14 Jan 03  (Deposition) - 09 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Ygiw, Structural Genomics, Hypothetical Protein, Ob-Fold, Structure 2 Function Project, S2F, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lehmann, A. Galkin, S. Pullalarevu, E. Sarikaya, W. Krajewski, K. Lim, A. Howard, O. Herzberg
Structure Of The Hypothetical Protein Ygiw From E. Coli.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YGIW
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYGIW
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PET100/D-TOPO
    Gene: YGIW
    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, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:29 , LYS A:32 , GLY A:62 , THR A:63 , HOH A:1036 , HOH A:1039 , HOH A:1082 , HOH A:1112BINDING SITE FOR RESIDUE SO4 A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NNX)

(-) 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:93
 aligned with YGIW_ECO57 | P0ADU6 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           YGIW_ECO57    23 QGGFSGPSATQSQAGGFQGPNGSVTTVESAKSLRDDTWVTLRGNIVERISDDLYVFKDASGTINVDIDHKRWNGVTVTPKDTVEIQGEVDKDWNSVEIDVKQIRKV 128
               SCOP domains d1nnxa_              A: Hypothetical protein YgiW                                                          SCOP domains
               CATH domains 1nnxA00              A:2-107 Hypothetical protein YgiW                                                     CATH domains
               Pfam domains -BOF-1nn             xA01 A:3-106                                                                        - Pfam domains
         Sec.struct. author ........-------------....hhhhhh.......eeeeeeeeeeee..eeeeee..eeeeee.hhhhh..........eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1nnx A   2 QGGFSGPS-------------GSVTTVESAKSLRDDTWVTLRGNIVERISDDLYVFKDASGTINVDIDHKRWNGVTVTPKDTVEIQGEVDKDWNSVEIDVKQIRKV 107
                                   | -         - |      31        41        51        61        71        81        91       101      
                                   9            23                                                                                    


Chain A from PDB  Type:PROTEIN  Length:93
 aligned with YGIW_ECOLI | P0ADU5 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           YGIW_ECOLI    23 QGGFSGPSATQSQAGGFQGPNGSVTTVESAKSLRDDTWVTLRGNIVERISDDLYVFKDASGTINVDIDHKRWNGVTVTPKDTVEIQGEVDKDWNSVEIDVKQIRKV 128
               SCOP domains d1nnxa_              A: Hypothetical protein YgiW                                                          SCOP domains
               CATH domains 1nnxA00              A:2-107 Hypothetical protein YgiW                                                     CATH domains
               Pfam domains -BOF-1nn             xA01 A:3-106                                                                        - Pfam domains
         Sec.struct. author ........-------------....hhhhhh.......eeeeeeeeeeee..eeeeee..eeeeee.hhhhh..........eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1nnx A   2 QGGFSGPS-------------GSVTTVESAKSLRDDTWVTLRGNIVERISDDLYVFKDASGTINVDIDHKRWNGVTVTPKDTVEIQGEVDKDWNSVEIDVKQIRKV 107
                                   | -         - |      31        41        51        61        71        81        91       101      
                                   9            23
   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: OB (224)

(-) Gene Ontology  (5, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YGIW_ECO57 | P0ADU6)
cellular component
    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).

Chain A   (YGIW_ECOLI | P0ADU5)
biological process
    GO:0071276    cellular response to cadmium ion    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 a cadmium (Cd) ion stimulus.
    GO:0070301    cellular response to hydrogen peroxide    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 a hydrogen peroxide (H2O2) stimulus.
    GO:0044011    single-species biofilm formation on inanimate substrate    A process in which microorganisms of the same species attach to and grow on an inanimate surface such as a rock or pipe, and produce extracellular polymers that facilitate attachment and matrix formation, resulting in an alteration in the phenotype of the organisms with respect to growth rate and gene transcription.
cellular component
    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

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(-) Related Entries Specified in the PDB File

ygiw