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(-) Description

Title :  SINGLE STRANDED DNA BINDING PROTEIN COMPLEX FROM HELICOBACTER PYLORI
 
Authors :  K. -W. Chan, C. -H. Wang, Y. -J. Lee, Y. -J. Sun
Date :  18 Jun 08  (Deposition) - 02 Jun 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Dna Replication, Single-Stranded Dna, Single-Stranded Dna Binding Protein, Oligonucleotide/Oligosaccharide Binding Fold, Helicobacter Pylori, Ob-Fold, Dna Damage, Dna Repair, Dna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. -W. Chan, Y. -J. Lee, C. -H. Wang, H. Huang, Y. -J. Sun
Single-Stranded Dna-Binding Protein Complex From Helicobacter Pylori Suggests An Ssdna-Binding Surface.
J. Mol. Biol. V. 388 508 2009
PubMed-ID: 19285993  |  Reference-DOI: 10.1016/J.JMB.2009.03.022

(-) Compounds

Molecule 1 - SINGLE-STRANDED DNA BINDING PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainSG13009
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-134
    Organism ScientificHELICOBACTER PYLORI
    Organism Taxid85962
    Strain26695
    SynonymSSB, HELIX-DESTABILIZING PROTEIN
 
Molecule 2 - POLY-DT
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2VW9)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VW9)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VW9)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SSBPS50935 Single-strand binding (SSB) domain profile.SSB_HELPY1-106
 
  2A:1001-1106
B:2001-2106
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SSBPS50935 Single-strand binding (SSB) domain profile.SSB_HELPY1-106
 
  4A:1001-1106
B:2001-2106

(-) Exons   (0, 0)

(no "Exon" information available for 2VW9)

(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:109
 aligned with SSB_HELPY | O25841 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:109
                                    10        20        30        40        50        60        70        80        90       100         
           SSB_HELPY      1 MFNKVIMVGRLTRNVELKYLPSGSAAATIGLATSRRFKKQDGTLGEEVCFIDARLFGRTAEIANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDKKS  109
               SCOP domains d2vw9a_ A: automated matches                                                                                  SCOP domains
               CATH domains 2vw9A00 A:1001-1109 Nucleic acid-binding proteins                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.............eeeeeeeeeeeeee.....eeeeeeeeeeeeehhhhhhhhhhh....eeeeeeeeeeeeee.....eeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SSB  PDB: A:1001-1106 UniProt: 1-106                                                                      --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                2vw9 A 1001 MFNKVIMVGRLTRNVELKYLPSGSAAATIGLATSRRFKKQDGTLGEEVCFIDARLFGRTAEIANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDKKS 1109
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100         

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with SSB_HELPY | O25841 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:106
                                    10        20        30        40        50        60        70        80        90       100      
           SSB_HELPY      1 MFNKVIMVGRLTRNVELKYLPSGSAAATIGLATSRRFKKQDGTLGEEVCFIDARLFGRTAEIANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMD  106
               SCOP domains d2vw9b_ B: automated matches                                                                               SCOP domains
               CATH domains 2vw9B00 B:2001-2106 Nucleic acid-binding proteins                                                          CATH domains
           Pfam domains (1) -SSB-2vw9B01 B:2002-2105                                                                                 - Pfam domains (1)
           Pfam domains (2) -SSB-2vw9B02 B:2002-2105                                                                                 - Pfam domains (2)
         Sec.struct. author ....eeeeeee.............eeeeeeeeeeeee.......eeeeeeeeeeeehhhhhhhhhhh....eeeeeeeeeeeeee.....eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SSB  PDB: B:2001-2106 UniProt: 1-106                                                                       PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                2vw9 B 2001 MFNKVIMVGRLTRNVELKYLPSGSAAATIGLATSRRFKKQDGTLGEEVCFIDARLFGRTAEIANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMD 2106
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      

Chain C from PDB  Type:DNA  Length:24
                                                         
                2vw9 C    1 TTTTTTTTTTTTTTTTTTTTTTTT   33
                                || |15||      26|   
                                5| 9| ||      26|   
                                 7 14 ||       30   
                                     16|            
                                      18            

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SSB_HELPY | O25841)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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