Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF GAMMA DELTA RESOLVASE
 
Authors :  B. Pan, G. P. Mullen
Date :  11 Jan 01  (Deposition) - 16 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (19x)
Keywords :  Recombinase, Catalytic Domain, Mixed Alpha Beta, Monomer, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pan, M. W. Maciejewski, A. Marintchev, G. P. Mullen
Solution Structure Of The Catalytic Domain Of Gammadelta Resolvase. Implications For The Mechanism Of Catalysis.
J. Mol. Biol. V. 310 1089 2001
PubMed-ID: 11501998  |  Reference-DOI: 10.1006/JMBI.2001.4821
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSPOSON GAMMA-DELTA RESOLVASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDJ1.3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL CATALYTIC DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  
NMR Structure (19x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1HX7)

(-) Sites  (0, 0)

(no "Site" information available for 1HX7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HX7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HX7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HX7)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RECOMBINASES_3PS51736 Resolvase/invertase-type recombinase catalytic domain profile.TNR1_ECOLI2-137  1A:2-105
2RECOMBINASES_1PS00397 Site-specific recombinases active site.TNR1_ECOLI6-14  1A:6-14
3RECOMBINASES_2PS00398 Site-specific recombinases signature 2.TNR1_ECOLI58-70  1A:58-70

(-) Exons   (0, 0)

(no "Exon" information available for 1HX7)

(-) Sequences/Alignments

NMR Structure
   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:105
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           TNR1_ECOLI     1 MRLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGK 105
               SCOP domains d1hx7a_ A: gamma,delta resolvase, catalytic domain                                                        SCOP domains
               CATH domains 1hx7A00 A:1-105  [code=3.40.50.1390, no name defined]                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhh.hhh.ee...........hhhhhhh.......eeee.............hhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -RECOMBINASES_3  PDB: A:2-105 UniProt: 2-137                                                              PROSITE (1)
                PROSITE (2) -----RECOMBINA-------------------------------------------RECOMBINASES_----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1hx7 A   1 MRLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGK 105
                                    10        20        30        40        50        60        70        80        90       100
   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  (1, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HX7)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (TNR1_ECOLI | P03012)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000150    recombinase activity    Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
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

NMR Structure
  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 1hx7)
 
  Sites
(no "Sites" information available for 1hx7)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hx7)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  1hx7
    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
  TNR1_ECOLI | P03012
    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)
  (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
  TNR1_ECOLI | P03012
    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
        TNR1_ECOLI | P03012: 1gdr 1gdt 1ght 1res 1ret 1zr2 1zr4 2gm4 2gm5 2rsl

(-) Related Entries Specified in the PDB File

4269 4269 IS THE 1H, 15N AND 13C CHEMICAL SHIFT ASSIGNMENTS FOR THE CATALYTIC CORE OF GAMMA DELTA RESOLVASE