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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF FIS BOUND TO 27 BP DNA F25 CONTAINING T2A3 SEQUENCE AT CENTER
 
Authors :  S. Stella, D. Cascio, R. C. Johnson
Date :  08 Sep 09  (Deposition) - 28 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hth Domain, Protein-Dna Complex, Minor Groove Compression, Dna Bending, Indirect Recognition, Activator, Dna-Binding, Transcription, Transcription Regulatio, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Stella, D. Cascio, R. C. Johnson
The Shape Of The Dna Minor Groove Directs Binding By The Dna-Bending Protein Fis.
Genes Dev. V. 24 814 2010
PubMed-ID: 20395367  |  Reference-DOI: 10.1101/GAD.1900610

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN FIS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FIS, B3261, JW3229
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
 
Molecule 2 - DNA (27-MER)
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (27-MER)
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3JRD)

(-) Sites  (0, 0)

(no "Site" information available for 3JRD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JRD)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3JRD)

(-) 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:91
 aligned with FIS_ECOLI | P0A6R3 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:91
                                    17        27        37        47        57        67        77        87        97 
             FIS_ECOLI    8 SDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN 98
               SCOP domains d3jrda_ A: FIS protein                                                                      SCOP domains
               CATH domains 3jrdA00 A:8-98 Homeodomain-like                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3jrd A  8 SDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN 98
                                    17        27        37        47        57        67        77        87        97 


Chain B from PDB  Type:PROTEIN  Length:98
 aligned with FIS_ECOLI | P0A6R3 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
             FIS_ECOLI    1 MFEQRVNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN 98
               SCOP domains d3jrdb_ B: FIS protein                                                                             SCOP domains
               CATH domains 3jrdB00 B:1-98 Homeodomain-like                                                                    CATH domains
           Pfam domains (1) -----------------------------------------------------HTH_8-3jrdB01 B:54-95                     --- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------HTH_8-3jrdB02 B:54-95                     --- Pfam domains (2)
         Sec.struct. author .....hhhhhheeeee.....eeeeehhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                  3jrd B  1 MFEQRVNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN 98
                                    10        20        30        40        50        60        70        80        90        


Chain C from PDB  Type:DNA  Length:27
                                                          
                  3jrd C  1 AAATTTGTTTGTTAAATGAGCAAATTT 27
                                    10        20       


Chain D from PDB  Type:DNA  Length:27
                                                          
                  3jrd D  1 AAATTTGCTCATTTAACAAACAAATTT 27
                                    10        20
   Legend:   → Mismatch (orange background)
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    → 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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FIS_ECOLI | P0A6R3)
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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000787    cytoplasmic nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the cytoplasm into higher order structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FIS_ECOLI | P0A6R3: 1etk 1eto 1etq 1etv 1etw 1etx 1ety 1f36 1fia 1fip 3fis 3iv5 3jr9 3jra 3jrb 3jrc 3jre 3jrf 3jrg 3jrh 3jri 4fis 5ds9 5dtd 5e3l 5e3m 5e3n 5e3o

(-) Related Entries Specified in the PDB File

3iv5 3jr9 3jra 3jrb 3jrc 3jre 3jrf 3jrg 3jrh 3jri