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(-) Description

Title :  CRYSTAL STRUCTURE OF THE I-LTRWI LAGLIDADG HOMING ENDONUCLEASE BOUND TO TARGET DNA.
 
Authors :  J. Chik, B. Shen, B. Stoddard
Date :  16 Jul 13  (Deposition) - 16 Jul 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ladlidadg, Protein-Dna Complex, Homing Endonuclease, Hydrolase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Chik, B. Shen, B. Stoddard
Structural Comparisons Of Laglidadg Homing Endonucleases.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LAGLIDADG HOMING ENDONUCLEASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: BL21 (DE3) RIL+
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMALL SUBUNIT RBOSOMAL RNA, MITOCHONDRIAL
    Organism Scientific: LEPTOGRAPHIUM TRUNCATUM
    Organism Taxid: 330483
    Strain: WIN(M)1435
    Synonym: LAGLIDADG HOMING ENDONUCLEASE I-LTRII
 
Molecule 2 - TOP STRAND DNA TARGET
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - BOTTOM STRAND DNA TARGET
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:22 , GLY A:180 , HOH A:509 , DG B:15 , DC C:15BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREALA A:21 , GLU A:181 , HOH A:507 , HOH A:508 , DT B:14 , DT C:16BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREGLU A:22 , GLU A:181 , DT B:14 , DG B:15 , DC C:15 , DT C:16BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREDT B:7 , DA B:9BINDING SITE FOR RESIDUE PEG B 101
5AC5SOFTWAREDA B:2 , DG B:3 , DG C:1 , DT C:24 , DG C:25 , DG C:26BINDING SITE FOR RESIDUE TRS C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LQ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LQ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LQ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LQ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4LQ0)

(-) 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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.eeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhh......ee.....eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh................hhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee.....eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lq0 A   7 NIEYLNWYICGLVDAEGSFGVNVVKHATNKTGYAVLTYFELAMNSKDKQLLELIKKTFDLECNIYHNPSDDTLKFKVSNIEQIVNKIIPFFEKYTLFSQKRGDFILFCKVVELIKNKEHLTLNGLMKILSIKAAMNLGLSENLKKEFPGCLSVKRPEFGLSNLNKRWLAGFIEGEACFFVSIYNSPKSKLGKAVQLVFKITQHIRDKILIESIVELLNCGRVEVRKSNEACDFTVTSIKEIENYIIPFFNEYPLIGQKLKNYEDFKLIFDMMKTKDHLTEEGLSKIIEIKNKMNTNRI 304
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296        


Chain B from PDB  Type:DNA  Length:26
                                                          
                 4lq0 B   1 CAGTAGTGAAGTATGTTATTTAACCC  26
                                    10        20      


Chain C from PDB  Type:DNA  Length:26
                                                          
                 4lq0 C   1 GGTTAAATAACATACTTCACTACTGG  26
                                    10        20
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  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 4LQ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LQ0)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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4lox