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(-) Description

Title :  STRUCTURE OF SOPB(155-323)-18MER DNA COMPLEX, I23 FORM
 
Authors :  M. A. Schumacher, K. Piro, W. Xu
Date :  15 Apr 10  (Deposition) - 05 May 10  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.86
Chains :  Asym. Unit :  B,P,T,U
Biol. Unit 1:  B,P,T,U  (1x)
Biol. Unit 2:  B (1x),P (1x),T (1x),U (1x)
Keywords :  Partition, F Plasmid, Sopb, Centromere, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, K. M. Piro, W. Xu
Insight Into F Plasmid Dna Segregation Revealed By Structures Of Sopb And Sopb-Dna Complexes.
Nucleic Acids Res. V. 38 4514 2010
PubMed-ID: 20236989  |  Reference-DOI: 10.1093/NAR/GKQ161

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')
    Chains: U, T
    Engineered: YES
    Other Details: THE DNA WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES
 
Molecule 2 - PROTEIN SOPB
    Chains: B, P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 155 TO 323
    Gene: B, ECOK12F047, PLASMID, SOPB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: PLASMID PARTITION PROTEIN B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : BPTU
Biological Unit 1 (1x): BPTU
Biological Unit 2 (1x): B (1x)P (1x)T (1x)U (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:201 , LEU B:202 , GLN B:225 , PHE B:228 , GLU B:232BINDING SITE FOR RESIDUE SO4 B 835
02AC2SOFTWAREARG B:219 , DC U:7BINDING SITE FOR RESIDUE SO4 B 836
03AC3SOFTWAREPRO P:203 , LYS P:204 , LYS P:236BINDING SITE FOR RESIDUE SO4 P 844
04AC4SOFTWAREARG P:219 , DC T:7BINDING SITE FOR RESIDUE SO4 P 846
05AC5SOFTWARELYS P:266 , THR P:267 , SER P:268BINDING SITE FOR RESIDUE SO4 P 849
06AC6SOFTWARESER P:189 , ARG P:190 , DC U:15BINDING SITE FOR RESIDUE SO4 P 945
07AC7SOFTWARESER B:189 , ARG B:190 , DC T:15BINDING SITE FOR RESIDUE SO4 B 936
08AC8SOFTWARELEU P:209 , PHE P:210 , SER P:211 , GLU P:215 , PHE P:252 , GLU P:253 , ALA P:254BINDING SITE FOR RESIDUE SO4 P 344
09AC9SOFTWARELYS P:201 , LEU P:202 , PHE P:228 , GLU P:232BINDING SITE FOR RESIDUE SO4 P 845
10BC1SOFTWAREPRO B:203 , LYS B:204 , SER B:205BINDING SITE FOR RESIDUE SO4 B 324

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MKY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MKY)

(-) Exons   (0, 0)

(no "Exon" information available for 3MKY)

(-) Sequences/Alignments

Asymmetric 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 B from PDB  Type:PROTEIN  Length:115
 aligned with SOPB_ECOLI | P62558 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:115
                                   166       176       186       196       206       216       226       236       246       256       266     
           SOPB_ECOLI   157 PTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDKEELLKQQASNLHEQKKAGVIFEAEEVITLLTSVLKTSSAS 271
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3mky B 157 PTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDKEELLKQQASNLHEQKKAGVIFEADEVITLLTSVLKTSSAS 271
                                   166       176       186       196       206       216       226       236       246       256       266     


Chain P from PDB  Type:PROTEIN  Length:114
 aligned with SOPB_ECOLI | P62558 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:114
                                   166       176       186       196       206       216       226       236       246       256       266    
           SOPB_ECOLI   157 PTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDKEELLKQQASNLHEQKKAGVIFEAEEVITLLTSVLKTSSA 270
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3mky P 157 PTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFSHPGELSARSGDALQKAFTDKEELLKQQASNLHEQKKAGVIFEADEVITLLTSVLKTSSA 270
                                   166       176       186       196       206       216       226       236       246       256       266    


Chain T from PDB  Type:DNA  Length:18
                                                  
                 3mky T   1 CTGGGACCATGGTCCCAG  18
                                    10        


Chain U from PDB  Type:DNA  Length:18
                                                  
                 3mky U   1 CTGGGACCATGGTCCCAG  18
                                    10
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3MKY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MKY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MKY)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain B,P   (SOPB_ECOLI | P62558)
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:0030541    plasmid partitioning    Any process in which plasmids are segregated or distributed into daughter cells upon cell division.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SOPB_ECOLI | P62558: 3kz5 3mkw 3mkz

(-) Related Entries Specified in the PDB File

3mkw SOPB(155-272)-18MER,I23 CRYSTAL FORM
3mkz SOPB(155-272)-18MER COMPLEX, P21 FORM