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(-) Description

Title :  CCDBVFI-FORMI-PH7.0
 
Authors :  N. De Jonge, L. Buts, R. Loris
Date :  10 Sep 09  (Deposition) - 01 Dec 09  (Release) - 23 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha+Beta, Sh3 Domain, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. De Jonge, W. Hohlweg, A. Garcia-Pino, M. Respondek, L. Buts, S. Haesaerts, J. Lah, K. Zangger, R. Loris
Structural And Thermodynamic Characterization Of Vibrio Fischeri Ccdb
J. Biol. Chem. V. 285 5606 2010
PubMed-ID: 19959472  |  Reference-DOI: 10.1074/JBC.M109.068429
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CCDB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: B462
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CCDB
    Organism Scientific: VIBRIO FISCHERI
    Organism Taxid: 668

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:2 , TYR A:7 , ASP A:30 , ARG A:35 , ASN A:92 , HOH A:116 , HOH A:132 , HOH A:140 , HOH A:161 , HOH A:169BINDING SITE FOR RESIDUE SO4 A 106

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JSC)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(no "Exon" information available for 3JSC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:96
 aligned with Q84B82_ALIFS | Q84B82 from UniProtKB/TrEMBL  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
         Q84B82_ALIFS     2 SQFTLYKNKDKSSAKTYPYFVDVQSDLLDNLNTRLVIPLTPIELLDKKAPSHLCPTIHIDEGDFIMLTQQMTSVPVKILSEPVNELSTFRNEIIAAIDFLITGI 105
               SCOP domains d3jsca_ A: CcdB                                                                                          SCOP domains
               CATH domains 3jscA00 A:2-105  [code=2.30.30.110, no name         defined]                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhh...eeee..hhhhh...eeeeeeeee...--------...eeee..eeeee.hhhheeee...eeeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3jsc A   2 SQFTLYKNKDKSSAKTYPYFVDVQSDLLDNLNTRLVIPLTPIEL--------LCPTIHIDEGDFIMLTQQMTSVPVKILSEPVNELSTFRNEIIAAIDFLITGI 105
                                    11        21        31        41   |     -  |     61        71        81        91       101    
                                                                      45       54
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 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 3JSC)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q84B82_ALIFS | Q84B82)
molecular function
    GO:0008657    DNA topoisomerase (ATP-hydrolyzing) inhibitor activity    Stops, prevents or reduces the activity of ATP-hydrolyzing DNA topoisomerase. ATP-hydrolyzing DNA topoisomerase catalyzes the DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
biological process
    GO:2000372    negative regulation of DNA topoisomerase (ATP-hydrolyzing) activity    Any process that stops, prevents or reduces the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity.
    GO:0006276    plasmid maintenance    The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.

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 Related Entries

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

UniProtKB/TrEMBL
        Q84B82_ALIFS | Q84B82: 2kmt 3jrz 3tcj 4ely

(-) Related Entries Specified in the PDB File

1vub CCDB DIMER
2vub CCDB DIMER
3jrz CCDBVFI STRUCTURE
3vub CCDB DIMER
4vub CCDB DIMER