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(-) Description

Title :  T. THERMOPHILUS RUVC IN COMPLEX WITH HOLLIDAY JUNCTION SUBSTRATE
 
Authors :  K. M. Gorecka, W. Komorowska, M. Nowotny
Date :  24 Jun 13  (Deposition) - 04 Sep 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.75
Chains :  Asym./Biol. Unit :  A,B,C,D,F
Keywords :  Rnase H Fold, Nuclease, Dna, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Gorecka, W. Komorowska, M. Nowotny
Crystal Structure Of Ruvc Resolvase In Complex With Hollida Junction Substrate.
Nucleic Acids Res. V. 41 9945 2013
PubMed-ID: 23980027  |  Reference-DOI: 10.1093/NAR/GKT769

(-) Compounds

Molecule 1 - CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC
    Chains: A, B
    EC Number: 3.1.22.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RUVC
    Gene: RUVC, TTHA1090
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579
    Synonym: HOLLIDAY JUNCTION NUCLEASE RUVC, HOLLIDAY JUNCTION RESOLVASE RUVC
 
Molecule 2 - DNA 31-MER
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 3 - DNA 13-MER
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 4 - DNA 11-MER
    Chains: F
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4LD0)

(-) Sites  (0, 0)

(no "Site" information available for 4LD0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LD0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:24 -Ala A:25
2Arg A:140 -Pro A:141
3Arg B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LD0)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4LD0)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ld0 A   1 MVVAGIDPGITHLGLGVVAVEGALKARLLHGEVVKTSPQEPAKERVGRIHARVLEVLHRFRPEAVAVQEQFFYRQNELAYKVGWALGAVLVAAFEAGVPVYAYGPMQVKQALAKEEVALMVRGILGLKEAPRPSHLADALAIALTHAFYARMGTAKPL 166
                                    10        20||      32        42        52        62        72        82        92       102       112  ||   128       138       148       158        
                                               21|                                                                                        115|                                            
                                                24                                                                                         122                                            


Chain B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeeeeee...eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ld0 B   0 HMVVAGIDPGITHLGLGVVAVLKARLLHGEVVKTSPQEPAKERVGRIHARVLEVLHRFRPEAVAVQEQFFYRQNELAYKVGWALGAVLVAAFEAGVPVYAYGPMQVKQALAAKEEVALMVRGILGLKEAPRPSHLADALAIALTHAFYARMGTAKPL 166
                                     9        19||      34        44        54        64        74        84        94       104       114||     129       139       149       159       
                                               20|                                                                                      115|                                             
                                                26                                                                                       121                                             


Chain C from PDB  Type:DNA  Length:31
                                                               
                 4ld0 C   1 CAATCGGCTTTGACCTTTGGTCAATCGGCAG  31
                                    10        20        30 


Chain D from PDB  Type:DNA  Length:13
                                             
                 4ld0 D   1 ATCTGCCGATTCT  13
                                    10   


Chain F from PDB  Type:DNA  Length:11
                                           
                 4ld0 F  22 GAAAGCCGATT  32
                                    31
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  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 4LD0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LD0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LD0)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:140 - Pro A:141   [ RasMol ]  
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    Gly A:24 - Ala A:25   [ RasMol ]  
 

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  4ld0
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 Related Entries

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

UniProtKB/Swiss-Prot
        RUVC_THET8 | Q5SJC4: 4ep4 4ep5

(-) Related Entries Specified in the PDB File

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