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(-) Description

Title :  X-RAY STRUCTURE OF ENDOLYSIN FROM CLOSTRIDIUM PERFRINGENS PHAGE PHISM101
 
Authors :  S. Kamitori, H. Yoshida
Date :  17 May 13  (Deposition) - 02 Apr 14  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta/Alpha Barrel, Muramidase And Putative Cell-Wall Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Tamai, H. Yoshida, H. Sekiya, H. Nariya, S. Miyata, A. Okabe, T. Kuwahara, J. Maki, S. Kamitori
X-Ray Structure Of A Novel Endolysin Encoded By Episomal Phage Phism101 Of Clostridium Perfringens
Mol. Microbiol. 2014
PubMed: search  |  Reference-DOI: 10.1111/MMI.12559

(-) Compounds

Molecule 1 - AUTOLYTIC LYSOZYME
    Chains: A, B
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD II
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CPR_C0050
    Organism Scientific: CLOSTRIDIUM PHAGE PHISM101
    Organism Taxid: 396359
    Strain: SM101

 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  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1ACT14Ligand/IonACETATE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MLA2Ligand/IonMALONIC ACID
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MLA1Ligand/IonMALONIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MLA1Ligand/IonMALONIC ACID

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:15 , TRP A:17 , LYS A:18 , GLU A:103 , TYR A:137 , TYR A:159 , GLU A:180 , ASP A:192 , HOH A:553 , HOH A:607 , HOH A:619 , HOH A:621 , HOH A:632BINDING SITE FOR RESIDUE EPE A 401
02AC2SOFTWAREASN A:222 , ARG A:224 , HOH A:649 , HOH A:692BINDING SITE FOR RESIDUE ACT A 402
03AC3SOFTWAREASN A:288 , ARG A:290 , HOH A:620 , HOH A:635 , HOH A:703 , HOH A:704 , LYS B:47BINDING SITE FOR RESIDUE MLA A 403
04AC4SOFTWAREVAL A:248 , GLY A:254 , TRP A:255 , ALA A:269BINDING SITE FOR RESIDUE ACT A 404
05AC5SOFTWARELEU A:209 , ASP A:210 , ARG A:310BINDING SITE FOR RESIDUE ACT A 405
06AC6SOFTWAREGLY A:74 , ALA A:75 , LYS A:76 , ASP A:77 , GLU A:119 , HOH A:598 , HOH A:665BINDING SITE FOR RESIDUE ACT A 406
07AC7SOFTWAREPHE A:207 , ASN A:211BINDING SITE FOR RESIDUE ACT A 407
08AC8SOFTWAREGLU A:40 , PHE A:44BINDING SITE FOR RESIDUE ACT A 408
09AC9SOFTWARETYR A:48 , GLN A:51 , HOH A:611BINDING SITE FOR RESIDUE ACT A 409
10BC1SOFTWAREGLY B:74 , ALA B:75 , LYS B:76 , ASP B:77BINDING SITE FOR RESIDUE ACT B 501
11BC2SOFTWAREMET B:1 , PRO B:164 , ASN B:167 , TRP B:170 , SER B:172 , TRP B:173 , HOH B:732BINDING SITE FOR RESIDUE ACT B 502
12BC3SOFTWARELYS B:220 , LEU B:221 , ASN B:222 , HOH B:688BINDING SITE FOR RESIDUE ACT B 503
13BC4SOFTWARESER B:15 , TRP B:17 , ASP B:192 , HOH B:658BINDING SITE FOR RESIDUE ACT B 504
14BC5SOFTWARELYS A:47 , HOH A:556 , LEU B:287 , ASN B:288 , ARG B:290 , TRP B:321 , HOH B:683 , HOH B:685 , HOH B:709BINDING SITE FOR RESIDUE MLA B 505
15BC6SOFTWAREVAL B:314 , GLY B:320 , TRP B:321 , TYR B:322BINDING SITE FOR RESIDUE ACT B 506
16BC7SOFTWAREGLY B:254 , ALA B:269BINDING SITE FOR RESIDUE ACT B 507
17BC8SOFTWARESER A:284 , TYR B:48 , GLN B:51 , HOH B:744BINDING SITE FOR RESIDUE ACT B 508

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KRT)

(-) 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.hhh....hhhhh.....eeeee...........hhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhh.........eeee........hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhh..hhhhh..eeee.................eeeee...........eeeeee.hhh...........eee.....eeeee.........eeeee....eeeee..hhh..eeeeee........hhheee..eeee.....eeeee.........eeeee....eeeee..hhh..eeeee.....eeeeehhheee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4krt A  -5 HHHHHMQSRNNNNLKGIDVSNWKGNINFESVKNDGVEVVYIKATEGNYFKDKYAKQNYEGAKEQGLSVGFYHFFRANKGAKDQANFFIDYLNEIGAVNYDCKLALDIETTEGVGVRDLTSMCIEFLEEVKRLTGKEVVVYTYTSFANNNLDSRLGNYPVWIAHYGVNTPGANNIWSSWVGFQYSENGSVAGVNGGCDMNEFTEEIFIDSSNFNLDNATTKNVSTKLNIRAKGTTNSKIIGSIPAGETFKIKWVDEDYLGWYYVEYNGVVGYVNADYVEKLQMATTYNVSTFLNVREEGSLNSRIVDKINSGDIFRIDWVDSDFIGWYRITTKNGKVGFVNAEFVKKL 342
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       
                               -1|                                                                                                                                                                                                                                                                                                                                                     
                                 1                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee.hhh....hhhhh.....eeeee...........hhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhh.........eeee........hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhh..hhhhh..eeee.................eeeee...........eee....hhh...........eee.....eeeee.........eeeee....eeeee..hhh..eeeeee........hhheee..eeee.....eeeee.........eeeee....eeeee..hhh..eeeee.....eeeeehhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4krt B   1 MQSRNNNNLKGIDVSNWKGNINFESVKNDGVEVVYIKATEGNYFKDKYAKQNYEGAKEQGLSVGFYHFFRANKGAKDQANFFIDYLNEIGAVNYDCKLALDIETTEGVGVRDLTSMCIEFLEEVKRLTGKEVVVYTYTSFANNNLDSRLGNYPVWIAHYGVNTPGANNIWSSWVGFQYSENGSVAGVNGGCDMNEFTEEIFIDSSNFNLDNATTKNVSTKLNIRAKGTTNSKIIGSIPAGETFKIKWVDEDYLGWYYVEYNGVVGYVNADYVEKLQMATTYNVSTFLNVREEGSLNSRIVDKINSGDIFRIDWVDSDFIGWYRITTKNGKVGFVNAEFVKKL 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4KRT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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