Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL BASIS FOR BROAD DNA-SPECIFICITY IN INTEGRON RECOMBINATION
 
Authors :  D. Macdonald, G. Demarre, M. Bouvier, D. Mazel, D. N. Gopaul
Date :  27 Jun 05  (Deposition) - 02 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein-Dna Complex, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Macdonald, G. Demarre, M. Bouvier, D. Mazel, D. N. Gopaul
Structural Basis For Broad Dna-Specificity In Integron Recombination.
Nature V. 440 1157 2006
PubMed-ID: 16641988  |  Reference-DOI: 10.1038/NATURE04643
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (31-MER)
    Chains: E, G
    Engineered: YES
    Other Details: SYTHETIC CONSTRUCT
    Synthetic: YES
 
Molecule 2 - DNA (34-MER)
    Chains: F, H
    Engineered: YES
    Other Details: SYTHETIC CONSTRUCT
    Synthetic: YES
 
Molecule 3 - SITE-SPECIFIC RECOMBINASE INTI4
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDG022 (PET DERIVED)
    Expression System Strain: BLI5
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: INTI4
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961
    Organism Taxid: 243277
    Strain: O1 BIOVAR ELTOR STR. N16961

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2A3V)

(-) Sites  (0, 0)

(no "Site" information available for 2A3V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A3V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A3V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A3V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A3V)

(-) Exons   (0, 0)

(no "Exon" information available for 2A3V)

(-) 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:313
 aligned with O68847_VIBCL | O68847 from UniProtKB/TrEMBL  Length:320

    Alignment length:319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311         
         O68847_VIBCL     2 KSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSRL 320
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........................hhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhh.hhh.ee....eeeeeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhh........eee....eee....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhh.------....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3v A   2 GSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTH------SGVLSPLSRL 320
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  |    311         
                                                                                                                                                                                                                                                                                                                                        304    311         


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with O68847_VIBCL | O68847 from UniProtKB/TrEMBL  Length:320

    Alignment length:320
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
         O68847_VIBCL     1 MKSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSRL 320
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhh.hhh.ee....eeee........eeee.hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhh...eeeeeee......eeeee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3v B   1 MGSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSRL 320
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320


Chain C from PDB  Type:PROTEIN  Length:317
 aligned with O68847_VIBCL | O68847 from UniProtKB/TrEMBL  Length:320

    Alignment length:320
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
         O68847_VIBCL     1 MKSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSRL 320
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........................hhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhh.hhh.ee....eeeeeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.hhhhhhhhh........eee....eee....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhh.---.......hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3v C   1 MGSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTH---RGASGVLSPLSRL 320
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300   |   310       320
                                                                                                                                                                                                                                                                                                                                         304 308            


Chain D from PDB  Type:PROTEIN  Length:320
 aligned with O68847_VIBCL | O68847 from UniProtKB/TrEMBL  Length:320

    Alignment length:320
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
         O68847_VIBCL     1 MKSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSRL 320
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhh.hhh.ee....eeee........eeee.hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhh...eeeeeee......eeeee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3v D   1 MGSQFLLSVREFMQTRYYAKKTIEAYLHWITRYIHFHNKKHPSLMGDKEVEEFLTYLAVQGKVATKTQSLALNSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGSGLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDLHQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSRL 320
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320


Chain E from PDB  Type:DNA  Length:31
                                                               
                 2a3v E   5 CCGGTTATAACGCCCGCCTAAGGGGCTGACA  35
                                    14        24        34 


Chain F from PDB  Type:DNA  Length:34
                                                                  
                 2a3v F   6 TGACAGTCCCTCTTGAGGCGTTTGTTATAACCGG  39
                                    15        25        35    


Chain G from PDB  Type:DNA  Length:29
                                                             
                 2a3v G   6 CGGTTATAACGCCCGCCTAAGGGGCTGAC  34
                                    15        25         


Chain H from PDB  Type:DNA  Length:32
                                                                
                 2a3v H   7 GACAGTCCCTCTTGAGGCGTTTGTTATAACCG  38
                                    16        26        36
   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 2A3V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A3V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A3V)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (O68847_VIBCL | O68847)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009009    site-specific recombinase activity    Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2a3v)
 
  Sites
(no "Sites" information available for 2a3v)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a3v)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2a3v
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O68847_VIBCL | O68847
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  O68847_VIBCL | O68847
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2A3V)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2A3V)