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(-) Description

Title :  CRYSTAL STRUCTURE OF LAGLIDADG MEGANUCLEASE I-PANMI WITH COORDINATED CALCIUM IONS
 
Authors :  J. P. Hallinan, B. L. Stoddard
Date :  16 Nov 15  (Deposition) - 30 Mar 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,G,H
Biol. Unit 1:  A,G,H  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Hydrolase-Dna Complex, Laglidadg, Homing Endonuclease, Meganuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Lambert, J. P. Hallinan, B. W. Shen, J. K. Chik, J. M. Bolduc, N. Kulshina, L. I. Robins, B. K. Kaiser, J. Jarjour, K. Havens, A. M. Scharenberg, B. L. Stoddard
Indirect Dna Sequence Recognition And Its Impact On Nucleas Cleavage Activity.
Structure V. 24 862 2016
PubMed-ID: 27133026  |  Reference-DOI: 10.1016/J.STR.2016.03.024

(-) Compounds

Molecule 1 - I-PANMI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 136-433
    Organism Common: PLEURAGE ANSERINA
    Organism Scientific: PODOSPORA ANSERINA
    Organism Taxid: 515849
    Strain: S / ATCC MYA-4624 / DSM 980 / FGSC 10383
 
Molecule 2 - DNA (27-MER)
    Chains: G, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (27-MER)
    Chains: H, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDGH
Biological Unit 1 (1x): A   GH
Biological Unit 2 (1x):  BCD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:20 , ALA A:176 , DC G:17 , DT H:16binding site for residue CA A 301
2AC2SOFTWAREGLY A:19 , GLU A:177 , DC G:16 , DA H:17binding site for residue CA A 302
3AC3SOFTWAREGLY B:19 , GLU B:177 , DC C:16 , DA D:17binding site for residue CA B 301
4AC4SOFTWAREGLU B:20 , ALA B:176 , DC C:17 , DT D:16binding site for residue CA B 302
5AC5SOFTWAREDT H:6binding site for residue GOL H 101
6AC6SOFTWAREDT D:6binding site for residue GOL D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ESP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr B:71 -Lys B:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ESP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ESP)

(-) Exons   (0, 0)

(no "Exon" information available for 5ESP)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.eeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee....eeeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.................hhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee...eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5esp A   7 KLNPSYISGFVDGEGSFMLTIIKDNKYKLGWRVVCRFVISLHKKDLSLLNKIKEFFDVGNVFLMTKDSAQYRVESLKGLDLIINHFDKYPLITKKQADYKLFKMAHNLIKNKSHLTKEGLLELVAIKAVINNGLNNDLSIAFPGINTILRPDTSLPQILNPFWLSGFVDAEGCFSVVVFKSKTSKLGEAVKLSFILTQSNRDEYLIKSLIEYLGCGNTSLDPRGTIDFKVTNFSSIKDIIVPFFIKYPLKGNKNLDFTDFCEVVRLMENKSHLTKEGLDQIKKIRNRMNTNR 298
                                    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:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.eeeeeeee.......eeeeeeeeeeehhhhhhhhhhhhhhhh..eeeee...eeeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.................hhhhhhhhhhhheeeeee.........eeeeeeeee..hhhhhhhhhhhhh..eeeee...eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5esp B   7 KLNPSYISGFVDGEGSFMLTIIKDNKYKLGWRVVCRFVISLHKKDLSLLNKIKEFFDVGNVFLMTKDSAQYRVESLKGLDLIINHFDKYPLITKKQADYKLFKMAHNLIKNKSHLTKEGLLELVAIKAVINNGLNNDLSIAFPGINTILRPDTSLPQILNPFWLSGFVDAEGCFSVVVTSKLGEAVKLSFILTQSNRDEYLIKSLIEYLGCGNTSLDPRGTIDFKVTNFSSIKDIIVPFFIKYPLKGNKNLDFTDFCEVVRLMENKSHLTKEGLDQIKKIRNRMNTNR 298
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       190       200       210       220       230       240       250       260       270       280       290        
                                                                                                                                                                                                           184|                                                                                                             
                                                                                                                                                                                                            189                                                                                                             


Chain C from PDB  Type:DNA  Length:26
                                                          
                 5esp C   1 CCCGCTCCTCATAATCCTTATCAAGC  26
                                    10        20      


Chain D from PDB  Type:DNA  Length:27
                                                           
                 5esp D   1 GGGCTTGATAAGGATTATGAGGAGCGG  27
                                    10        20       


Chain G from PDB  Type:DNA  Length:27
                                                           
                 5esp G   1 CCCGCTCCTCATAATCCTTATCAAGCC  27
                                    10        20       


Chain H from PDB  Type:DNA  Length:27
                                                           
                 5esp H   1 GGGCTTGATAAGGATTATGAGGAGCGG  27
                                    10        20
   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  (0, 0)

(no "SCOP Domain" information available for 5ESP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ESP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ESP)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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