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(-) Description

Title :  THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)
 
Authors :  R. Molina, S. Stella, P. Redondo, H. Gomez, M. J. Marcaida, M. Orozco, J. G. Montoya
Date :  26 May 14  (Deposition) - 17 Dec 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,K,M,O
Biol. Unit 1:  A,B,C,K  (1x)
Biol. Unit 2:  G,H,I,O  (1x)
Biol. Unit 3:  D,E,F,M  (1x)
Keywords :  Hydrolase-Dna Complex, Catalysis, Protein-Dna Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Molina, S. Stella, P. Redondo, H. Gomez, M. J. Marcaida, M. Orozco, J. Prieto, G. Montoya
Visualizing Phosphodiester-Bond Hydrolysis By An Endonuclease.
Nat. Struct. Mol. Biol. V. 22 65 2015
PubMed-ID: 25486305  |  Reference-DOI: 10.1038/NSMB.2932

(-) Compounds

Molecule 1 - HOMING ENDONUCLEASE I-DMOI
    Chains: A, D, G
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector: PET24D
    Expression System Vector Type: PLASMID
    Organism Scientific: DESULFUROCOCCUS MOBILIS
    Organism Taxid: 2274
    Synonym: I-DMOI
 
Molecule 2 - 25MER
    Chains: B, E, H
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
    Chains: C, F, I
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
    Chains: K, M, O
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIKMO
Biological Unit 1 (1x): ABC      K  
Biological Unit 2 (1x):       GHI  O
Biological Unit 3 (1x):    DEF    M 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1MN9Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , ALA A:116 , LYS A:120 , HOH A:2003 , DA B:14 , DC K:16BINDING SITE FOR RESIDUE MN A1188
2AC2SOFTWAREGLY A:20 , GLU A:117 , HOH A:2002 , HOH A:2035 , DG B:15 , DC C:15BINDING SITE FOR RESIDUE MN A1189
3AC3SOFTWAREGLY D:20 , GLU D:117 , ASN D:129 , HOH D:2002 , HOH D:2003 , DG E:15 , DC F:15BINDING SITE FOR RESIDUE MN D1189
4AC4SOFTWAREASP D:21 , ALA D:116 , HOH D:2004 , DA E:14 , DC M:16BINDING SITE FOR RESIDUE MN D1190
5AC5SOFTWAREASP G:21 , GLN G:42 , ALA G:116 , HOH G:2002 , DA H:14 , DC O:16BINDING SITE FOR RESIDUE MN G1180
6AC6SOFTWAREGLY G:20 , GLU G:117 , MN G:1182 , HOH G:2001 , HOH G:2030 , DG H:15 , DC I:15BINDING SITE FOR RESIDUE MN G1181
7AC7SOFTWAREASP D:21 , GLU D:117 , DA E:14 , DG E:15 , DC F:15 , DC M:16BINDING SITE FOR RESIDUE MN D1191
8AC8SOFTWAREASP A:21 , GLU A:117 , DA B:14 , DG B:15 , DC C:15 , DC K:16BINDING SITE FOR RESIDUE MN A1190
9AC9SOFTWAREASP G:21 , GLU G:117 , MN G:1181 , DA H:14 , DG H:15 , DC I:15 , DC O:16BINDING SITE FOR RESIDUE MN G1182

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys D:30 -Gly D:31
2Gly D:31 -Asn D:32
3Lys G:30 -Gly G:31
4Gly G:31 -Asn G:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UNA)

(-) Sequences/Alignments

Asymmetric 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:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhh....eeeeeee....eeeeee...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4una A   4 NENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP 187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    


Chain B from PDB  Type:DNA  Length:25
                                                         
                 4una B   1 GCCTTGCCGGGTAAGTTCCGGCGCG  25
                                    10        20     


Chain C from PDB  Type:DNA  Length:15
                                               
                 4una C   1 CGCGCCGGAACTTAC  15
                                    10     


Chain D from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4una D   4 NENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP 187
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183    


Chain E from PDB  Type:DNA  Length:25
                                                         
                 4una E   1 GCCTTGCCGGGTAAGTTCCGGCGCG  25
                                    10        20     


Chain F from PDB  Type:DNA  Length:15
                                               
                 4una F   1 CGCGCCGGAACTTAC  15
                                    10     


Chain G from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4una G   4 NENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILS 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      


Chain H from PDB  Type:DNA  Length:25
                                                         
                 4una H   1 GCCTTGCCGGGTAAGTTCCGGCGCG  25
                                    10        20     


Chain I from PDB  Type:DNA  Length:15
                                               
                 4una I   1 CGCGCCGGAACTTAC  15
                                    10     


Chain K from PDB  Type:DNA  Length:10
                                          
                 4una K  16 CCGGCAAGGC  25
                                    25


Chain M from PDB  Type:DNA  Length:10
                                          
                 4una M  16 CCGGCAAGGC  25
                                    25


Chain O from PDB  Type:DNA  Length:10
                                          
                 4una O  16 CCGGCAAGGC  25
                                    25
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    → 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 4UNA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  4una
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        DMO1_DESMO | P21505: 1b24 1mow 2vs7 2vs8 4d6n 4d6o 4un7 4un8 4un9 4unb 4unc 4ut0 5a0w 5ak9 5akf 5akm 5akn

(-) Related Entries Specified in the PDB File

4un6 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7)
4un7 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA BEFORE INCUBATION IN 5MM MN (STATE 1)
4un8 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2)
4un9 THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8H INCUBATION IN 5MM MN (STATE 3)
4unb THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 6 DAYS INCUBATION IN 5MM MN (STATE 5)
4unc THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8 DAYS INCUBATION IN 5MM MN (STATE 6)