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(-) Description

Title :  ANABAENA HU-DNA COCRYSTAL STRUCTURE (AHU2)
 
Authors :  K. S. Swinger, K. M. Lemberg, Y. Zhang, P. A. Rice
Date :  30 Apr 03  (Deposition) - 13 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Dna Bending, Hu, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. S. Swinger, K. M. Lemberg, Y. Zhang, P. A. Rice
Flexible Dna Bending In Hu-Dna Cocrystal Structures
Embo J. V. 22 3749 2003
PubMed-ID: 12853489  |  Reference-DOI: 10.1093/EMBOJ/CDG351

(-) Compounds

Molecule 1 - 5'-D(*TP*GP*CP*AP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP *AP*CP*C)-3'
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED DNA
    Synthetic: YES
 
Molecule 2 - DNA-BINDING PROTEIN HU
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A (PETAHU)
    Expression System Strain: RJ1878 LACKS FUNCTIONAL HU GENES
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HUP OR HANA OR ASR3935
    Organism Scientific: ANABAENA SP.
    Organism Taxid: 1167

 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 1P78)

(-) Sites  (0, 0)

(no "Site" information available for 1P78)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P78)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P78)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P78)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_LIKEPS00045 Bacterial histone-like DNA-binding proteins signature.DBH_NOSS146-65
 		  2A:46-65
B:46-65

(-) Exons   (0, 0)

(no "Exon" information available for 1P78)

(-) 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:92
 aligned with DBH_NOSS1 | P05514 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
             DBH_NOSS1    1 MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFSAGKLFREKVAPP 92
               SCOP domains d1p78a_ A: HU protein                                                                        SCOP domains
               CATH domains 1p78A00 A:1-92 HU Protein, subunit A                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------HISTONE_LIKE        --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  1p78 A  1 MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFSAGKLFREKVAPP 92
                                    10        20        30        40        50        60        70        80        90  


Chain B from PDB  Type:PROTEIN  Length:92
 aligned with DBH_NOSS1 | P05514 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
             DBH_NOSS1    1 MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFSAGKLFREKVAPP 92
               SCOP domains d1p78b_ B: HU protein                                                                        SCOP domains
               CATH domains 1p78B00 B:1-92 HU Protein, subunit A                                                         CATH domains
           Pfam domains (1) Bac_DNA_binding-1p78B01 B:1-90                                                            -- Pfam domains (1)
           Pfam domains (2) Bac_DNA_binding-1p78B02 B:1-90                                                            -- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee...eeeeeeee..eeee......eeee..eeeeeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------HISTONE_LIKE        --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  1p78 B  1 MNKGELVDAVAEKASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAFSAGKLFREKVAPP 92
                                    10        20        30        40        50        60        70        80        90  


Chain C from PDB  Type:DNA  Length:20
                                                   
                  1p78 C  1 TGCATATCAATTTGTTGCAC 20
                                    10        20


Chain D from PDB  Type:DNA  Length:21
                                                    
                  1p78 D  1 TGCATATCAATTTGTTGCACC 21
                                    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: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Bac_DNA_binding] (8)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DBH_NOSS1 | P05514)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
    GO:0043158    heterocyst differentiation    The process in which a relatively unspecialized cell acquires specialized features of a heterocyst, a differentiated cell in certain cyanobacteria whose purpose is to fix nitrogen.

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  1p78
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 Related Entries

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

UniProtKB/Swiss-Prot
        DBH_NOSS1 | P05514: 1p51 1p71

(-) Related Entries Specified in the PDB File

1b8z THERMOTOGA MARITIMA PROTEIN ALONE
1ihf E. COLI IHF BOUND TO DNA
1p51 ANABAENA HU BOUND TO AHU6 DNA
1p71 ANABAENA HU BOUND TO TR3 DNA