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(-) Description

Title :  CRYSTAL STRUCTURE OF A LSR-DNA COMPLEX
 
Authors :  K. Rutherford, P. Yuan, K. Perry, G. D. Van Duyne
Date :  02 May 13  (Deposition) - 10 Jul 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,E,F  (1x)
Biol. Unit 2:  B,G,H  (1x)
Biol. Unit 3:  C,I,J  (1x)
Biol. Unit 4:  D,K,L  (1x)
Keywords :  Recombinase Domain, Zinc-Ribbon Domain, Coiled-Coil Motif, Recombination-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Rutherford, P. Yuan, K. Perry, R. Sharp, G. D. Van Duyne
Attachment Site Recognition And Regulation Of Directionalit By The Serine Integrases.
Nucleic Acids Res. V. 41 8341 2013
PubMed-ID: 23821671  |  Reference-DOI: 10.1093/NAR/GKT580

(-) Compounds

Molecule 1 - PUTATIVE INTEGRASE [BACTERIOPHAGE A118]
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: INT
    Organism Scientific: LISTERIA INNOCUA
    Organism Taxid: 272626
    Strain: CLIP 11262
 
Molecule 2 - DNA (26-MER)
    Chains: E, G, I, K
    Engineered: YES
    Fragment: ATTP LEFT HALF SITE TOP STRAND
    Other Details: ATTP HALF-SITE
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: F, H, J, L
    Engineered: YES
    Fragment: ATTP LEFT HALF SITE BOTTOM STRAND
    Other Details: ATTP HALF-SITE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): A   EF      
Biological Unit 2 (1x):  B    GH    
Biological Unit 3 (1x):   C     IJ  
Biological Unit 4 (1x):    D      KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:274 , LYS A:276 , CYS A:277 , CYS A:302 , CYS A:314BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS A:455 , HIS A:457 , HIS A:459 , ASP D:330BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREHIS A:458 , HIS A:460 , HIS D:455 , HIS D:459BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWAREASN A:334BINDING SITE FOR RESIDUE CA A 505
5AC5SOFTWARECYS B:274 , LYS B:276 , CYS B:277 , CYS B:302 , CYS B:314BINDING SITE FOR RESIDUE ZN B 501
6AC6SOFTWARECYS C:274 , LYS C:276 , CYS C:277 , CYS C:302 , CYS C:314BINDING SITE FOR RESIDUE ZN C 501
7AC7SOFTWARECYS D:274 , LYS D:276 , CYS D:277 , CYS D:302 , CYS D:314BINDING SITE FOR RESIDUE ZN D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KIS)

(-) 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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.............eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhh.eeee...eeee.......hhhhhhhhhhhhhhhhhh..............eee......eeeeeeeeee..eeeeeeeeee.hhh............eehhhhhhhhhhhhhhhhhhh..ee.hhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhheeeeeee..eeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kis A 134 DRMVMGKIKRIEAGLPLTTAKGRTFGYDVIDTKLYINEEEAKQLRLIYDIFEEEQSITFLQKRLKKLGFKVRTYNRYNNWLTNDLYCGYVSYKDKVHVKGIHEPIISEEQFYRVQEIFSRMGKNPNMNKESASLLNNLVVCSKCGLGFVHRRKDTVSRGKKYHYRYYSCKTYKHTHELEKCGNKIWRADKLEELIIDRVNNYSFASRNIDKEDESLNEKLKIEHAKKKRLFDLYINGSYEVSELDSMMNDIDAQINYYEAQIEANEELKKNKTVDFNSLEFREKQLYLKSLINKIYIDGEQVTIEWLLEHHHHHH 460
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   ||  355       365       375       385       395       405 ||    425       435       445       455     
                                                                                                                                                                                                                                               347|                                                      407|                                          
                                                                                                                                                                                                                                                350                                                       418                                          


Chain B from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.............eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhh.eeee...eeee.......hhhhhhhhhhhhhhhhhh..............eee......eeeeeeeeee..eeeeeeeeee.hhh............eehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.eeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kis B 134 DRMVMGKIKRIEAGLPLTTAKGRTFGYDVIDTKLYINEEEAKQLRLIYDIFEEEQSITFLQKRLKKLGFKVRTYNRYNNWLTNDLYCGYVSYKDKVHVKGIHEPIISEEQFYRVQEIFSRMGKNPNMNKESASLLNNLVVCSKCGLGFVHRRKDTVSRGKKYHYRYYSCKTYKHTHELEKCGNKIWRADKLEELIIDRVNNYSFELDSLNEKLKIEHAKKKRLFDLYSELDSMMNDIDAQINYYEAQIEANEELKKNKKIQENLADLATVDFNSLEFREKQLYLKSLINKIYIDGEQVTIEWLLE 454
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333   ||  352       362      |379       389       399       409       419       429       439       449     
                                                                                                                                                                                                                                     337|                   369|                                                                             
                                                                                                                                                                                                                                      347                    377                                                                             


Chain C from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.......eeee...eeee.......hhhhhhhhhhhhhhhh................eee......eeeeee..ee..ee..eeeeee.hhh............eehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhheeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kis C 134 DRMVMGKIKRIEAGLPLTTAKGRTFGYDVIDTKLYINEEEAKQLRLIYDIFEEEQSITFLQKRLKKLGFKVRTYNRYNNWLTNDLYCGYVSYKDKVHVKGIHEPIISEEQFYRVQEIFSRMGKNPNMNKESASLLNNLVVCSKCGLGFVHRRKDTVSRGKKYHYRYYSCKTYKHTHELEKCGNKIWRADKLEELIIDRVNNYSFASRNIDKEDELDSLNEKLKIEHAKKKRLFDLYDSMMNDIDAQINYYEAQIEANEELKKNKKIQENLADLATVDFNSLEFREKQLYLKSLINKIYIDGEQVTIEWL 452
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363     ||383       393       403       413       423       433       443         
                                                                                                                                                                                                                                                                     369|                                                                        
                                                                                                                                                                                                                                                                      380                                                                        


Chain D from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.............eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhh.eeee...eeee.......hhhhhhhhhhhhhhhhhh..............eee......eeeeee..ee..ee..eeeeee.hhh............eehhhhhhhhhhhhh......hhhhhh.hhhhh....hhhhhh.....hhhhh............hhhhhhhhhhhhh.eeeee..eeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kis D 133 RDRMVMGKIKRIEAGLPLTTAKGRTFGYDVIDTKLYINEEEAKQLRLIYDIFEEEQSITFLQKRLKKLGFKVRTYNRYNNWLTNDLYCGYVSYKDKVHVKGIHEPIISEEQFYRVQEIFSRMGKNPNMNKESASLLNNLVVCSKCGLGFVHRRKDTVSRGKKYHYRYYSCKTYKHTHELEKCGNKIWRADKLEELIIDRVNNYSFASRNIDKELNEKLKIEIDAQINYYEAQIEANEELKKNKKIQEFNSLEFREKQLYLKSLINKIYIDGEQVTIEWLLEHHHHHH 460
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342  ||   357||     394       404      |423       433       443       453       
                                                                                                                                                                                                                                              345|    358|                      411|                                       
                                                                                                                                                                                                                                               351     386                       421                                       


Chain E from PDB  Type:DNA  Length:26
                                                          
                 4kis E  25 GTTTAGTTCCTCGTTTTCTCTCGTTG  50
                                    34        44      


Chain F from PDB  Type:DNA  Length:26
                                                          
                 4kis F  -1 CCAACGAGAGAAAACGAGGAACTAAA  24
                                     8        18      


Chain G from PDB  Type:DNA  Length:26
                                                          
                 4kis G  25 GTTTAGTTCCTCGTTTTCTCTCGTTG  50
                                    34        44      


Chain H from PDB  Type:DNA  Length:26
                                                          
                 4kis H  -1 CCAACGAGAGAAAACGAGGAACTAAA  24
                                     8        18      


Chain I from PDB  Type:DNA  Length:26
                                                          
                 4kis I  25 GTTTAGTTCCTCGTTTTCTCTCGTTG  50
                                    34        44      


Chain J from PDB  Type:DNA  Length:26
                                                          
                 4kis J  -1 CCAACGAGAGAAAACGAGGAACTAAA  24
                                     8        18      


Chain K from PDB  Type:DNA  Length:26
                                                          
                 4kis K  25 GTTTAGTTCCTCGTTTTCTCTCGTTG  50
                                    34        44      


Chain L from PDB  Type:DNA  Length:26
                                                          
                 4kis L  -1 CCAACGAGAGAAAACGAGGAACTAAA  24
                                     8        18
   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 4KIS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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  Q928V6_LISIN | Q928V6
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        Q928V6_LISIN | Q928V6: 5u96 5uae 5udo

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