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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE PYOCIN S2 NUCLEASE DOMAIN, IMMUNITY PROTEIN COMPLEX AT 1.8 ANGSTROMS
 
Authors :  R. Grinter, I. Josts, A. W. Roszak, C. J. Cogdell, D. Walker
Date :  07 Jun 14  (Deposition) - 10 Jun 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Hnh Nuclease Domain, Colicin Nuclease Immunity Protein Complex, Bacteriocin, Bacterial Cytotoxin, Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Grinter, I. Josts, L. C. Mccaughey, A. W. Roszak, K. I. Walen, S. Kelly, O. Byron, D. Walker
Structural Insights Into Pyocin S2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYOCIN-S2 IMMUNITY PROTEIN
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Gene: IMM2
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
 
Molecule 2 - PYOCIN-S2
    Chains: B, D, F, H
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Fragment: NUCLEASE DOMAIN, C-TERMINAL FRAGEMENT RESIDUES 556-689
    Gene: PYS2
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: KILLER PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 39)

Asymmetric Unit (2, 39)
No.NameCountTypeFull Name
1BR35Ligand/IonBROMIDE ION
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:65 , ALA A:66 , HOH A:254BINDING SITE FOR RESIDUE BR A 101
02AC2SOFTWAREGLU A:10 , LYS A:11 , HOH A:223BINDING SITE FOR RESIDUE BR A 102
03AC3SOFTWAREGLY A:83 , PHE A:84 , HOH A:204BINDING SITE FOR RESIDUE BR A 103
04AC4SOFTWARETRP B:604 , ILE B:655BINDING SITE FOR RESIDUE BR B 701
05AC5SOFTWAREARG B:642BINDING SITE FOR RESIDUE BR B 702
06AC6SOFTWAREGLY B:666 , VAL B:667 , THR H:566 , HOH H:801BINDING SITE FOR RESIDUE BR B 703
07AC7SOFTWAREHIS B:656 , HIS B:681 , HOH B:876BINDING SITE FOR RESIDUE MG B 704
08AC8SOFTWAREALA C:66 , HOH C:271BINDING SITE FOR RESIDUE BR C 101
09AC9SOFTWARELYS C:11BINDING SITE FOR RESIDUE BR C 102
10BC1SOFTWARELYS C:73 , GLY C:83 , PHE C:84BINDING SITE FOR RESIDUE BR C 103
11BC2SOFTWARETRP D:604 , ILE D:655BINDING SITE FOR RESIDUE BR D 701
12BC3SOFTWAREARG D:642BINDING SITE FOR RESIDUE BR D 702
13BC4SOFTWAREGLY D:666 , VAL D:667 , ASN F:669 , HOH F:801BINDING SITE FOR RESIDUE BR D 703
14BC5SOFTWAREPRO D:558 , ARG D:559 , HOH D:864BINDING SITE FOR RESIDUE BR D 704
15BC6SOFTWAREARG D:660 , ILE D:661 , BR D:706 , HOH D:864BINDING SITE FOR RESIDUE BR D 705
16BC7SOFTWAREILE D:661 , ALA D:662 , BR D:705BINDING SITE FOR RESIDUE BR D 706
17BC8SOFTWAREHIS D:656 , HIS D:681 , HIS D:685 , HOH D:829BINDING SITE FOR RESIDUE MG D 707
18BC9SOFTWAREARG D:559 , ILE D:655 , HIS D:657BINDING SITE FOR RESIDUE BR D 708
19CC1SOFTWAREPRO E:65 , ALA E:66 , HOH E:273BINDING SITE FOR RESIDUE BR E 101
20CC2SOFTWARELYS E:11 , HOH E:278BINDING SITE FOR RESIDUE BR E 102
21CC3SOFTWAREPHE E:84BINDING SITE FOR RESIDUE BR E 103
22CC4SOFTWARETRP F:604 , ARG F:608 , ILE F:655BINDING SITE FOR RESIDUE BR F 701
23CC5SOFTWAREHOH E:295 , ARG F:642BINDING SITE FOR RESIDUE BR F 702
24CC6SOFTWARETHR D:566 , HOH D:939 , GLY F:666 , VAL F:667BINDING SITE FOR RESIDUE BR F 703
25CC7SOFTWAREPRO F:558 , ARG F:559 , HOH F:874BINDING SITE FOR RESIDUE BR F 704
26CC8SOFTWAREARG F:660 , ILE F:661 , BR F:706 , HOH F:874BINDING SITE FOR RESIDUE BR F 705
27CC9SOFTWAREILE F:661 , ALA F:662 , BR F:705BINDING SITE FOR RESIDUE BR F 706
28DC1SOFTWAREHIS F:656 , HIS F:681 , HIS F:685 , HOH F:805BINDING SITE FOR RESIDUE MG F 707
29DC2SOFTWARETRP F:576 , LEU F:577 , GLN F:624BINDING SITE FOR RESIDUE BR F 708
30DC3SOFTWARELYS G:18 , ALA G:66BINDING SITE FOR RESIDUE BR G 101
31DC4SOFTWARETHR G:9 , GLU G:10 , LYS G:11BINDING SITE FOR RESIDUE BR G 102
32DC5SOFTWAREGLY G:83 , PHE G:84 , HOH G:213BINDING SITE FOR RESIDUE BR G 103
33DC6SOFTWARETRP H:604 , ILE H:655BINDING SITE FOR RESIDUE BR H 701
34DC7SOFTWAREARG H:642BINDING SITE FOR RESIDUE BR H 702
35DC8SOFTWARETHR B:566 , HOH B:862 , VAL H:667BINDING SITE FOR RESIDUE BR H 703
36DC9SOFTWAREASP H:557 , PRO H:558 , ARG H:559 , HOH H:886BINDING SITE FOR RESIDUE BR H 704
37EC1SOFTWAREARG H:660 , ILE H:661 , BR H:706 , HOH H:886BINDING SITE FOR RESIDUE BR H 705
38EC2SOFTWAREALA H:662 , BR H:705BINDING SITE FOR RESIDUE BR H 706
39EC3SOFTWAREHIS H:656 , HIS H:681 , HIS H:685 , HOH H:802BINDING SITE FOR RESIDUE MG H 707

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QKO)

(-) 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:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4qko A   1 MKSKISEYTEKEFLEFVKDIYTNNKKKFPTEESHIQAVLEFKKLTEHPSGSDLLYYPNENREDSPAGVVKEVKEWRASKGLPGFKAG  87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhh.......eeee..hhhhh....hhh.eeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qko B 556 RDPRDVPGAATGKGQPVSGNWLGAASQGEGAPIPSQIADKLRGKTFKNWRDFREQFWIAVANDPELSKQFNPGSLAVMRDGGAPYVRESEQAGGRIKIEIHHKVRIADGGGVYNMGNLVAVTPKRHIEIHK 686
                                   565       575       585       595       605       615       625       635       645       655       665       675       685 


Chain C from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4qko C   1 MKSKISEYTEKEFLEFVKDIYTNNKKKFPTEESHIQAVLEFKKLTEHPSGSDLLYYPNENREDSPAGVVKEVKEWRASKGLPGFKAG  87
                                    10        20        30        40        50        60        70        80       


Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh.......eeee..hhhhh....hhh.eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qko D 556 RDPRDVPGAATGKGQPVSGNWLGAASQGEGAPIPSQIADKLRGKTFKNWRDFREQFWIAVANDPELSKQFNPGSLAVMRDGGAPYVRESEQAGGRIKIEIHHKVRIADGGGVYNMGNLVAVTPKRHIEIHKGG 688
                                   565       575       585       595       605       615       625       635       645       655       665       675       685   


Chain E from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4qko E   1 MKSKISEYTEKEFLEFVKDIYTNNKKKFPTEESHIQAVLEFKKLTEHPSGSDLLYYPNENREDSPAGVVKEVKEWRASKGLPGFKAG  87
                                    10        20        30        40        50        60        70        80       


Chain F from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh.......eeee..hhhhh....hhh.eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qko F 556 RDPRDVPGAATGKGQPVSGNWLGAASQGEGAPIPSQIADKLRGKTFKNWRDFREQFWIAVANDPELSKQFNPGSLAVMRDGGAPYVRESEQAGGRIKIEIHHKVRIADGGGVYNMGNLVAVTPKRHIEIHK 686
                                   565       575       585       595       605       615       625       635       645       655       665       675       685 


Chain G from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4qko G   2 KSKISEYTEKEFLEFVKDIYTNNKKKFPTEESHIQAVLEFKKLTEHPSGSDLLYYPNENREDSPAGVVKEVKEWRASKGLPGFKAG  87
                                    11        21        31        41        51        61        71        81      


Chain H from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh.......eeee..hhhhh....hhh.eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qko H 556 RDPRDVPGAATGKGQPVSGNWLGAASQGEGAPIPSQIADKLRGKTFKNWRDFREQFWIAVANDPELSKQFNPGSLAVMRDGGAPYVRESEQAGGRIKIEIHHKVRIADGGGVYNMGNLVAVTPKRHIEIHK 686
                                   565       575       585       595       605       615       625       635       645       655       665       675       685
   Legend:   → Mismatch (orange background)
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  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 '|'

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(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3u43 COLICIN E2 NUCLEASE, IMMUNITY PROTEIN COMPLEX
7cei COLICIN E7 NUCLEASE, IMMUNITY PROTEIN COMPLEX