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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PYOCIN L1 AT 2.09 ANGSTROMS
 
Authors :  R. Grinter, A. W. Roszak, L. Mccaughey, R. J. Cogdell, D. Walker
Date :  25 Jun 13  (Deposition) - 19 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Monocot Mannose Binding Lectin, Mmbl, Galanthus Nivalis Agglutinin, Gna, Beta Prism, Bacteriocin, Protein Antimicrobial, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Mccaughey, R. Grinter, I. Josts, A. W. Roszak, K. I. Walen, R. J. Cogdell, J. Milner, T. Evans, S. Kelly, N. P. Tucker, O. Byron, B. Smith, D. Walker
Lectin-Like Bacteriocins From Pseudomonas Spp. Utilise D-Rhamnose Containing Lipopolysaccharide As A Cellular Receptor.
Plos Pathog. V. 10 03898 2014
PubMed-ID: 24516380  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003898

(-) Compounds

Molecule 1 - PYOCIN L1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 1333543
    Strain: C 1433

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 45)

Asymmetric Unit (2, 45)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO42Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 28)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO28Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO14Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (44, 44)

Asymmetric Unit (44, 44)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:123 , THR A:245 , THR A:246 , EDO A:303 , HOH A:457BINDING SITE FOR RESIDUE EDO A 301
02AC2SOFTWAREALA A:2 , SER A:4 , GLN A:9 , LEU A:243 , ASP A:244 , THR A:245 , HOH A:510BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREGLU A:89 , TYR A:91 , ASN A:123 , ILE A:125 , EDO A:301 , HOH A:478BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREPRO A:20 , ASN A:21 , LYS A:23 , ASP A:96 , GLN A:239 , HOH A:492BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREPRO A:20 , GLN A:95 , ASP A:96 , GLY A:238 , GLN A:239 , SER A:250 , HOH A:506BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWARELYS A:124 , ILE A:139 , HOH A:512 , HOH A:557BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREGLN A:9 , LYS A:122 , CL A:329 , HOH A:572 , GLN B:161BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREASP A:88 , HOH A:572BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWARELYS A:231 , THR B:47 , THR B:48 , VAL B:50 , ALA B:72 , TRP B:73BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWAREGLY A:200 , PRO A:232BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWAREPRO A:43 , ASN A:46 , THR A:48 , PRO A:49 , EDO A:317 , CL A:330BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWARELYS A:108 , TRP A:109 , THR A:195 , HIS A:196 , HOH A:430 , HOH A:520 , HOH A:542 , HIS B:196 , EDO B:307BINDING SITE FOR RESIDUE EDO A 312
13BC4SOFTWAREALA A:107 , GLY A:110 , ILE A:112BINDING SITE FOR RESIDUE EDO A 313
14BC5SOFTWARELEU A:36 , GLY A:98 , LYS A:225BINDING SITE FOR RESIDUE EDO A 314
15BC6SOFTWARELYS A:67 , GLY A:69 , VAL A:133 , ARG A:174 , HOH A:431 , HOH A:482 , HOH A:555BINDING SITE FOR RESIDUE EDO A 315
16BC7SOFTWAREVAL A:10 , LYS A:55 , GLU A:59 , TYR A:65 , HOH A:416 , HOH A:450 , HOH A:479BINDING SITE FOR RESIDUE EDO A 316
17BC8SOFTWARETHR A:47 , THR A:48 , VAL A:50 , ALA A:72 , TRP A:73 , EDO A:311 , EDO A:318BINDING SITE FOR RESIDUE EDO A 317
18BC9SOFTWAREVAL A:50 , ASN A:66 , ALA A:72 , EDO A:317 , HOH A:580BINDING SITE FOR RESIDUE EDO A 318
19CC1SOFTWAREVAL A:71 , HOH A:428BINDING SITE FOR RESIDUE EDO A 319
20CC2SOFTWARETYR A:143 , ILE A:164 , THR A:210 , LYS A:212 , HOH A:440 , HOH A:574BINDING SITE FOR RESIDUE EDO A 320
21CC3SOFTWARETHR A:41 , VAL A:50 , ASN A:66 , LYS A:67 , ALA A:68 , HOH A:576 , HOH A:580BINDING SITE FOR RESIDUE EDO A 321
22CC4SOFTWARELYS A:25 , GLY A:40 , PRO A:52 , HOH A:496BINDING SITE FOR RESIDUE EDO A 322
23CC5SOFTWAREGLN A:15 , PHE A:16 , EDO A:324BINDING SITE FOR RESIDUE EDO A 323
24CC6SOFTWAREEDO A:323 , HOH A:581BINDING SITE FOR RESIDUE EDO A 324
25CC7SOFTWAREARG A:12 , GLN A:15 , HOH A:432 , HOH A:581BINDING SITE FOR RESIDUE EDO A 325
26CC8SOFTWAREASP A:13BINDING SITE FOR RESIDUE EDO A 326
27CC9SOFTWAREVAL A:113 , SER A:115BINDING SITE FOR RESIDUE EDO A 327
28DC1SOFTWAREGLN A:148 , ASP A:150 , ASN A:152 , TYR A:156BINDING SITE FOR RESIDUE EDO A 328
29DC2SOFTWARELYS A:122 , THR A:245 , EDO A:307 , GLN B:161BINDING SITE FOR RESIDUE CL A 329
30DC3SOFTWARETRP A:45 , ASN A:46 , EDO A:311BINDING SITE FOR RESIDUE CL A 330
31DC4SOFTWARESER B:3 , PRO B:20 , ASN B:93 , LEU B:94 , ILE B:248 , TRP B:249 , HOH B:456 , HOH B:524BINDING SITE FOR RESIDUE EDO B 301
32DC5SOFTWAREGLN B:161 , HOH B:528BINDING SITE FOR RESIDUE EDO B 302
33DC6SOFTWAREGLN B:148 , ASN B:152 , TYR B:156 , HOH B:420 , HOH B:513BINDING SITE FOR RESIDUE EDO B 303
34DC7SOFTWARESER B:4 , GLN B:9 , LEU B:243 , ASP B:244 , THR B:245 , THR B:246 , EDO B:309BINDING SITE FOR RESIDUE EDO B 304
35DC8SOFTWAREALA B:6 , THR B:245 , EDO B:309BINDING SITE FOR RESIDUE EDO B 305
36DC9SOFTWAREEDO A:312 , HOH A:520 , HIS B:194 , EDO B:308BINDING SITE FOR RESIDUE EDO B 307
37EC1SOFTWAREHOH A:542 , ALA B:191 , LEU B:192 , HIS B:194 , EDO B:307BINDING SITE FOR RESIDUE EDO B 308
38EC2SOFTWAREPRO B:7 , GLN B:9 , EDO B:304 , EDO B:305BINDING SITE FOR RESIDUE EDO B 309
39EC3SOFTWAREALA B:191 , HOH B:459BINDING SITE FOR RESIDUE EDO B 310
40EC4SOFTWARETYR A:78 , THR A:79 , ALA A:80 , TRP B:45 , LEU B:224BINDING SITE FOR RESIDUE EDO B 311
41EC5SOFTWAREASP B:88 , GLU B:89 , PRO B:117 , GLU B:118BINDING SITE FOR RESIDUE EDO B 312
42EC6SOFTWAREGLU B:89 , LEU B:114 , LYS B:206 , PHE B:214 , EDO B:314 , HOH B:478 , HOH B:493BINDING SITE FOR RESIDUE EDO B 313
43EC7SOFTWAREVAL B:113 , LEU B:114 , EDO B:313 , HOH B:542BINDING SITE FOR RESIDUE EDO B 314
44EC8SOFTWAREGLN B:9 , VAL B:10BINDING SITE FOR RESIDUE CL B 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LE7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:159 -Pro A:160
2Asn B:159 -Pro B:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LE7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LE7)

(-) Exons   (0, 0)

(no "Exon" information available for 4LE7)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....ee....eee.....eeeee.....eeeee...eeeee........eeee...eeee.....eeee........hhhhhhh.eeee.....eeee.....ee............eeee....ee....eeee..eeeee.....eeeee....eeeee.......eeee.....eeeee..eeeee.........eeeee....eeee...eeee...ee.......ee...........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le7 A   2 ASSLAPRQVIRDGQFITSPNGKYKLVMQADGNLVLYEDGTKPIWNTTPVGPGAKAVMEFNLNLYNKAGQVAWSSNVYTAYLFEEFKDEAYLNLQDDGDFGIFSDEAKWGSIVLSRPEVGVKNKIIPTGTVMVPGTEYINGNYRLAFQGDGNLVIYQINPQVVIWATYTMGADRAVVQEDGNFVIYKGTTALWHTHTATGMPAYLKFTNTGKLFLSQPTLLWTLKRGSLSKPPKVIPGQHGPLDTTPIWSWPHDY 255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251    


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....ee...eeee.....eeeee.....eeeee...eeeee........eeee...eeee.....eeee..........hhhhhheeee.....eeee...eeee............eeee....ee...eeeee..eeeee.....eeeee....eeeee.......eeee.....eeeee..eeeee.........eeeee....eeee...eeee...ee.......ee...........ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4le7 B   2 ASSLAPRQVIRDGQFITSPNGKYKLVMQADGNLVLYEDGTKPIWNTTPVGPGAKAVMEFNLNLYNKAGQVAWSSNVYTAYLFEEFKDEAYLNLQDDGDFGIFSDEAKWGSIVLSRPEVGVKNKIIPTGTVMVPGTEYINGNYRLAFQGDGNLVIYQINPQVVIWATYTMGADRAVVQEDGNFVIYKGTTALWHTHTATGMPAYLKFTNTGKLFLSQPTLLWTLKRGSLSKPPKVIPGQHGPLDTTPIWSWPHD 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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 4LE7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LE7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LE7)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4LE7)

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 Related Entries

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        T2LG16_PSEAI | T2LG16: 4lea 4led

(-) Related Entries Specified in the PDB File

4lea PYOCIN L1 BOUND TO D-MANNOSE 2.55 ANGSTROMS
4led PYOCIN L1 BOUND TO D-RHAMNOSE AT 2.37 ANGSTROMS