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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PRIMASE REPB' IN COMPLEX WITH INITIATOR DNA
 
Authors :  S. Geibel, S. Banchenko, M. Engel, E. Lanka, W. Saenger
Date :  14 Apr 09  (Deposition) - 28 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Protein-Dna-Complex, Hairpin Dna, Mixed Alpha-Beta Fold, Primase, Rsf1010, Replication, Replication-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Geibel, S. Banchenko, M. Engel, E. Lanka, W. Saenger
Structure And Function Of Primase Repb' Encoded By Broad-Host-Range Plasmid Rsf1010 That Replicates Exclusivel In Leading-Strand Mode
Proc. Natl. Acad. Sci. Usa V. 106 7810 2009
PubMed-ID: 19416864  |  Reference-DOI: 10.1073/PNAS.0902910106

(-) Compounds

Molecule 1 - REPLICATION PROTEIN B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-212
    Gene: REPB
    Organism Scientific: PLASMID RSF1010
    Organism Taxid: 2504
 
Molecule 2 - SINGLE STRANDED INITIATOR DNA (SSIA)
    Chains: C
    Engineered: YES
    Fragment: SINGLE STRANDED INITIATOR DNA, GB 2701-2727
    Other Details: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3H25)

(-) Sites  (0, 0)

(no "Site" information available for 3H25)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H25)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:154 -Lys A:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H25)

(-) Exons   (0, 0)

(no "Exon" information available for 3H25)

(-) 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:188
 aligned with Q52349_ECOLX | Q52349 from UniProtKB/TrEMBL  Length:323

    Alignment length:195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     
         Q52349_ECOLX     4 DRTLQAIGRQLKAMGCERFDIGVRDATTGQMMNREWSAAEVLQNTPWLKRMNAQGNDVYIRPAEQERHGLVLVDDLSEFDLDDMKAEGREPALVVETSPKNYQAWVKVADAAGGELRGQIARTLASEYDADPASADSRHYGRLAGFTNRKDKHTTRAGYQPWVLLRESKGKTATAGPALVQQAGQQIEQAQRQQE 198
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhh.eeeeeee.......eeeeeeehhhhhhhhhhh.....eeeeee..eeeeeee.....hhhhhhhhhhhhhhhh..hhhhh.....ee..........-------....eeee.......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h25 A   4 DRTLQAIGRQLKAMGCERFDIGVRDATTGQMMNREWSAAEVLQNTPWLKRMNAQGNDVYIRPAEQERHGLVLVDDLSEFDLDDMKAEGREPALVVETSPKNYQAWVKVADAAGGELRGQIARTLASEYDADPASADSRHYGRLAGFTNRKDK-------QPWVLLRESKGKTATAGPALVQQAGQQIEQAQRQQE 198
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 |     163       173       183       193     
                                                                                                                                                                                 155     163                                   


Chain C from PDB  Type:DNA  Length:27
                                                           
                 3h25 C   1 CCTTTCCCCCTACCCGAAGGGTGGGGG  27
                                    10        20
   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  (0, 0)

(no "SCOP Domain" information available for 3H25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H25)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  Sites
(no "Sites" information available for 3h25)
 
  Cis Peptide Bonds
    Asp A:154 - Lys A:155   [ RasMol ]  
 

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  3h25
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 Related Entries

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

UniProtKB/TrEMBL
        Q52349_ECOLX | Q52349: 3h20

(-) Related Entries Specified in the PDB File

3h20