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(-) Description

Title :  I-MSOI RE-DESIGNED FOR ALTERED DNA CLEAVAGE SPECIFICITY (-8GCG)
 
Authors :  G. K. Taylor, B. L. Stoddard
Date :  11 Apr 10  (Deposition) - 19 May 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Homing Nuclease, Rosetta Design, De Novo Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ashworth, G. K. Taylor, J. J. Havranek, S. A. Quadri, B. L. Stoddard, D. Baker
Computational Reprogramming Of Homing Endonuclease Specificity At Multiple Adjacent Base Pairs.
Nucleic Acids Res. V. 38 5601 2010
PubMed-ID: 20435674  |  Reference-DOI: 10.1093/NAR/GKQ283

(-) Compounds

Molecule 1 - MSO-8G
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: ARTIFICIAL GENE
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
 
Molecule 2 - DNA (5'- D(*GP*CP*AP*GP*GP*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*CP*TP*CP* CP*G)-3')
    Chains: C
    Engineered: YES
    Other Details: TOP STRAND OLIGONUCLEOTIDE TARGET
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*GP*GP*AP*GP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*GP*CP*CP*TP* GP*C)-3')
    Chains: D
    Engineered: YES
    Other Details: BOTTOM STRAND OLIGONUCLEOTIDE TARGET
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:22 , GLY B:21 , DG C:3 , DC D:2BINDING SITE FOR RESIDUE CA A 2
2AC2SOFTWAREGLY A:21 , ASP B:22 , HOH B:168 , HOH B:190 , DA C:2 , DG D:3 , CA D:13BINDING SITE FOR RESIDUE CA B 3
3AC3SOFTWAREASP A:22 , CA B:3 , ASP B:22 , DA C:2 , DG C:3 , DC D:2 , DG D:3BINDING SITE FOR RESIDUE CA D 13

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MIP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MIP)

(-) 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    
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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:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeeeeeeee........eeeeeeeeeeee...hhhhhhhhhhh....ee.......eeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mip A   6 TLQPTEAAYIAGFLDGDGSIYARLEPRPDYKDIKYQVRLAISFIQRKDKFPYLQDIYDQLGKRGILRKDRGDGIADYRIYGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 


Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeeeeeeee........eeeeeeeeeeee..hhhhhhhhhhhh....ee.......eeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mip B   6 TLQPTEAAYIAGFLDGDGSIYARLEPRPDYKDIKYQVRLAISFIQRKDKFPYLQDIYDQLGKRGILRKDRGDGIADYRIYGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKI 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 


Chain C from PDB  Type:DNA  Length:24
                                                        
                 3mip C -12 GCAGGCGGTCGTGAGACCGCTCCG  12
                                    -3 ||      8    
                                      -1|           
                                        1           


Chain D from PDB  Type:DNA  Length:24
                                                        
                 3mip D -12 CGGAGCGGTCTCACGACCGCCTGC  12
                                    -3 ||      8    
                                      -1|           
                                        1
   Legend:   → Mismatch (orange background)
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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 3MIP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

3ko2 3mis