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

(-) Description

Title :  CRYSTAL STRUCTURE OF A DELETION MUTANT OF DEINOCOCCUS RADIODURANS RECN
 
Authors :  S. Pellegrino, J. Radzimanowski, D. De Sanctis, S. Mcsweeney, J. Timm
Date :  22 Dec 11  (Deposition) - 12 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Binding Protein, Dna Repair, Atpase Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pellegrino, J. Radzimanowski, D. De Sanctis, E. B. Erba, S. Mcsweeney, J. Timmins
Structural And Functional Characterization Of An Smc-Like Protein Recn: New Insights Into Double-Strand Break Repair.
Structure V. 20 2076 2012
PubMed-ID: 23085075  |  Reference-DOI: 10.1016/J.STR.2012.09.010

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RECN
    Chains: A
    EC Number: 3.6.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: STAR
    Expression System Vector: PET151-TOPO
    Expression System Vector Type: PLASMID
    Fragment: HEAD AND PARTIAL COILED-COIL DOMAINS, RESIDUES 1-237,305-564
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: R1
    Synonym: RECOMBINATION PROTEIN N, RECN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4AD8)

(-) Sites  (0, 0)

(no "Site" information available for 4AD8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AD8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:331 -Pro A:332
2Asp A:523 -Gly A:524

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AD8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AD8)

(-) Exons   (0, 0)

(no "Exon" information available for 4AD8)

(-) 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:452
 aligned with RECN_DEIRA | Q9WXF2 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:532
                                    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       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561  
           RECN_DEIRA    32 PRLSRLEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGGRANHDLIRSGEKELLVTGFWGDGDESEADSASRRLSSAGRGAARLSGEVVSVRELQEWAQGRLTIHWQHSAVSLLSPANQRGLLDRRVTKEAQAYAAAHAAWREAVSRLERLQASQRERARQIDLLAFQVQEISEVSPDPGEEEGLNTELSRLSNLHTIAQAAAGGVELLSDGDLNAAGLIGEAVRALNAGAKYDETVMQLQNELRAALESVQAIAGELRDVAEGSAADPEALDRVEARLSALSKLKNKYGPTLEDVVEFGAQAAEELAGLEEDERDAGSLQADVDALHAELLKVGQALDAAREREAEPLVDSLLAVIRELGMPHARMEFALSALAEPAAYGLSDVLLRFSANPGEELGPLSDVASGGELSRVMLAVSTVLGADTPSVVFDEVDAGIGGAAAIAVAEQLSRLADTRQVLVVTHLAQIAARAHHHYKVEKQVEDGRTVSHVRLLTGDERLEEIARMLSGNTSEAALEHARELLA 563
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......eeee....eeeeeehhhhhhhhhhhhhhhhh....hhhh......eeeeeee.--------.eeeeeee.....eee......hhhhhhhhhh..eeeehhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh------------------------------------------------------------------------..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee.........eeeeeeee................hhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhheeeee..hhhhhhhh.eeeeee..ee..ee..eeee..hhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ad8 A  32 PRLSRLEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGGRANHDLIRSGEKELLVTGFW--------DSASRRLSSAGRGAARLSGEVVSVRELQEWAQGRLTIHWQHSAVSLLSPANQRGLLDRRVTKEAQAYAAAHAAWREAVSRLERLQASQRERARQIDLLAFQVQEISEVSPDPGEEEGLNTELSRLSNLH------------------------------------------------------------------------PEALDRVEARLSALSKLKNKYGPTLEDVVEFGAQAAEELAGLEEDERDAGSLQADVDALHAELLKVGQALDAAREREAEPLVDSLLAVIRELGMPHARMEFALSALAEPAAYGLSDVLLRFSANPGEELGPLSDVASGGELSRVMLAVSTVLGADTPSVVFDEVDAGIGGAAAIAVAEQLSRLADTRQVLVVTHLAQIAARAHHHYKVEKQVEDGRTVSHVRLLTGDERLEEIARMLSGNTSEAALEHARELLA 563
                                    41        51        61        71        81        91        |-       111       121       131       141       151       161       171       181       191       201       211       221       231     |   -         -         -         -         -         -         -       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561  
                                                                                              100      109                                                                                                                             237                                                                      310
   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 4AD8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AD8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AD8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RECN_DEIRA | Q9WXF2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    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.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

 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 4ad8)
 
  Sites
(no "Sites" information available for 4ad8)
 
  Cis Peptide Bonds
    Asp A:523 - Gly A:524   [ RasMol ]  
    Gly A:331 - Pro A:332   [ RasMol ]  
 

(-) 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
  4ad8
    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
  RECN_DEIRA | Q9WXF2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.3
    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
  RECN_DEIRA | Q9WXF2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RECN_DEIRA | Q9WXF2: 4abx 4aby

(-) Related Entries Specified in the PDB File

4abx CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS RECN COILED- COIL DOMAIN
4aby CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS RECN HEAD DOMAIN