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(-) Description

Title :  STRUCTURE OF OKRAI/DNA COMPLEX
 
Authors :  E. S. Vanamee, A. K. Aggarwal
Date :  11 Aug 10  (Deposition) - 06 Oct 10  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Alpha And Beta Proteins (A/B), Restriction Endonuclease-Like, Phosphodiesterase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Vanamee, H. Viadiu, S. H. Chan, A. Ummat, A. M. Hartline, S. Y. Xu, A. K. Aggarwal
Asymmetric Dna Recognition By The Okrai Endonuclease, An Isoschizomer Of Bamhi.
Nucleic Acids Res. V. 39 712 2011
PubMed-ID: 20833632  |  Reference-DOI: 10.1093/NAR/GKQ779

(-) Compounds

Molecule 1 - OKRAI ENDONUCLEASE
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Organism Scientific: OCEANOBACTER KRIEGII
    Organism Taxid: 64972
    Strain: NEB STRAIN COLLECTION
 
Molecule 2 - DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
    Chains: C, D, G, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:86 , TRP A:100 , HOH A:262 , HOH A:640 , DG D:5 , HOH D:254BINDING SITE FOR RESIDUE CA A 195
2AC2SOFTWAREGLU A:71 , ASP A:86 , HOH A:200 , HOH A:228 , HOH A:343 , DG D:4 , DG D:5 , HOH D:258BINDING SITE FOR RESIDUE CA A 196
3AC3SOFTWAREASP B:86 , GLU B:99 , HOH B:196 , HOH B:655 , DG C:5 , HOH C:256BINDING SITE FOR RESIDUE CA B 195
4AC4SOFTWAREASP E:86 , TRP E:100 , HOH E:197 , HOH E:665 , DG H:5 , HOH H:35BINDING SITE FOR RESIDUE CA E 195
5AC5SOFTWAREASP F:86 , GLU F:99 , HOH F:612 , HOH F:613 , HOH F:634 , DG G:5BINDING SITE FOR RESIDUE CA F 195
6AC6SOFTWAREGLU E:71 , ASP E:86 , HOH E:220 , HOH E:705 , HOH E:706 , DG H:4 , DG H:5BINDING SITE FOR RESIDUE CA H 13

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Trp A:34 -Pro A:35
2Pro B:16 -Gly B:17
3Trp B:34 -Pro B:35
4Trp E:34 -Pro E:35
5Trp F:34 -Pro F:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ODH)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....hhhhhhhhhhhhhhh..........ee........hhhhhhhhhhhhhhh..eeee............eeeeee....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.......hhhhhh.hhhhhh......eeeeeeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3odh A   1 MKIKRIEVLINNGSVPGIPMILNEIQDAIKTVSWPEGNNSFVINPVRKGNGVKPIKNSCMRHLHQKGWALEHPVRIKAEMRPGPLDAVKMIGGKAFALEWETGNISSSHRAINKMVMGMLERVIIGGVLILPSRDMYNYLTDRVGNFRELEPYFSVWRQFNLKDAYLAIVEIEHDSVDAQVSLIPKGTDGRAIR 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee.....hhhhhhhhhhhhhhh.........ee.........hhhhhhhhhhhhhh..eeeeee........eeeeeeee....eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhh.......hhhhhh.hhhhhh......eeeeeeeee..ee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3odh B   1 MKIKRIEVLINNGSVPGIPMILNEIQDAIKTVSWPEGNNSFVINPVRKGNGVKPIKNSCMRHLHQKGWALEHPVRIKAEMRPGPLDAVKMIGGKAFALEWETGNISSSHRAINKMVMGMLERVIIGGVLILPSRDMYNYLTDRVGNFRELEPYFSVWRQFNLKDAYLAIVEIEHDSVDAQVSLIPKGTDGRA 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  


Chain C from PDB  Type:DNA  Length:12
                                            
                 3odh C   1 TATGGATCCATA  12
                                    10  


Chain D from PDB  Type:DNA  Length:12
                                            
                 3odh D   1 TATGGATCCATA  12
                                    10  


Chain E from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.....hhhhhhhhhhhhhhh..........ee............hhhhhhhhhhh..eeee............eeeeee....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.......hhhhhh.hhhhhh.......eeeeeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3odh E   1 MKIKRIEVLINNGSVPGIPMILNEIQDAIKTVSWPEGNNSFVINPVRKGNGVKPIKNSCMRHLHQKGWALEHPVRIKAEMRPGPLDAVKMIGGKAFALEWETGNISSSHRAINKMVMGMLERVIIGGVLILPSRDMYNYLTDRVGNFRELEPYFSVWRQFNLKDAYLAIVEIEHDSVDAQVSLIPKGTDGRAIR 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain F from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....hhhhhhhhhhhhhhh..........ee........hhhhhhhhhhhhhhh.....eee........eee..eeee..eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhh.......hhhhhh.hhhhhh......eeeeeeeee..ee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3odh F   1 MKIKRIEVLINNGSVPGIPMILNEIQDAIKTVSWPEGNNSFVINPVRKGNGVKPIKNSCMRHLHQKGWALEHPVRIKAEMRPGPLDAVKMIGGKAFALEWETGNISSSHRAINKMVMGMLERVIIGGVLILPSRDMYNYLTDRVGNFRELEPYFSVWRQFNLKDAYLAIVEIEHDSVDAQVSLIPKGTDGRAIR 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain G from PDB  Type:DNA  Length:12
                                            
                 3odh G   1 TATGGATCCATA  12
                                    10  


Chain H from PDB  Type:DNA  Length:12
                                            
                 3odh H   1 TATGGATCCATA  12
                                    10
   Legend:   → Mismatch (orange background)
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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 3ODH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ODH)

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