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(-) Description

Title :  CRYSTAL STRUCTURE OF PLIC-ST, PERIPLASMIC LYSOZYME INHIBITOR OF C-TYPE LYSOZYME FROM SALMONELLA TYPHIMURIUM
 
Authors :  S. Leysen, J. M. Van Herreweghe, L. Callewaert, M. Heirbaut, P. Buntin C. W. Michiels, S. V. Strelkov
Date :  12 Aug 10  (Deposition) - 22 Dec 10  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Beta Barrel, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Leysen, J. M. Van Herreweghe, L. Callewaert, M. Heirbaut, P. Buntinx, C. W. Michiels, S. V. Strelkov
Molecular Basis Of Bacterial Defense Against Host Lysozymes X-Ray Structures Of Periplasmic Lysozyme Inhibitors Plii An Plic.
J. Mol. Biol. V. 405 1233 2011
PubMed-ID: 21146533  |  Reference-DOI: 10.1016/J.JMB.2010.12.007

(-) Compounds

Molecule 1 - PUTATIVE PERIPLASMIC PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: STM1249
    Organism Scientific: SALMONELLA ENTERICA
    Organism Taxid: 90371

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C   
Biological Unit 2 (1x):  B D  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 35)

Asymmetric Unit (2, 35)
No.NameCountTypeFull Name
1MSE29Mod. Amino AcidSELENOMETHIONINE
2NA6Ligand/IonSODIUM ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:86BINDING SITE FOR RESIDUE NA A 6
2AC2SOFTWAREGLN B:27 , GLU B:28 , ILE B:29 , SER B:30 , ASN C:37 , HOH C:123 , HOH C:125BINDING SITE FOR RESIDUE NA C 4
3AC3SOFTWAREGLN C:27 , ASN C:48BINDING SITE FOR RESIDUE NA C 5
4AC4SOFTWAREASN D:114BINDING SITE FOR RESIDUE NA E 3
5AC5SOFTWARELYS C:71BINDING SITE FOR RESIDUE NA F 1

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:36 -A:110
2B:36 -B:110
3C:36 -C:110
4D:36 -D:110
5E:36 -E:110
6F:36 -F:110

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser C:74 -Gly C:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OE3)

(-) Exons   (0, 0)

(no "Exon" information available for 3OE3)

(-) 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:85
 aligned with Q8ZPY8_SALTY | Q8ZPY8 from UniProtKB/TrEMBL  Length:114

    Alignment length:87
                                    36        46        56        66        76        86        96       106       
         Q8ZPY8_SALTY    27 QEISKSIYTCNDNQVMEVIYVNTEAGNAYAIISQVNEMIPMRLMKMASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLA 113
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeee.....eeeeeee..eeeeeeeee.--.eeeee.......eeeee..eeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3oe3 A  27 QEISKSIYTCNDNQVmEVIYVNTEAGNAYAIISQVNEmIPmRLmKm--GANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLA 113
                                    36     |  46        56       |66|  | |  76        86        96       106       
                                          42-MSE                64-MSE | | 75                                      
                                                                   67-MSE|                                         
                                                                      70-MSE                                       
                                                                        72-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with Q8ZPY8_SALTY | Q8ZPY8 from UniProtKB/TrEMBL  Length:114

    Alignment length:87
                                    36        46        56        66        76        86        96       106       
         Q8ZPY8_SALTY    27 QEISKSIYTCNDNQVMEVIYVNTEAGNAYAIISQVNEMIPMRLMKMASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLA 113
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeee.....eeeeeee..eeeeeeeee.---.eeee.......eeeee..eeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3oe3 B  27 QEISKSIYTCNDNQVmEVIYVNTEAGNAYAIISQVNEmIPmRLmKm---ANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLA 113
                                    36     |  46        56       |66|  | |  76        86        96       106       
                                          42-MSE                64-MSE | |  76                                     
                                                                   67-MSE|                                         
                                                                      70-MSE                                       
                                                                        72-MSE                                     


Chain C from PDB  Type:PROTEIN  Length:88
 aligned with Q8ZPY8_SALTY | Q8ZPY8 from UniProtKB/TrEMBL  Length:114

    Alignment length:88
                                    36        46        56        66        76        86        96       106        
         Q8ZPY8_SALTY    27 QEISKSIYTCNDNQVMEVIYVNTEAGNAYAIISQVNEMIPMRLMKMASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLAN 114
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhheeeeeeeee.....eeeeeee..eeeeeee......eeeee.......eeeee..eeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3oe3 C  27 QEISKSIYTCNDNQVmEVIYVNTEAGNAYAIISQVNEmIPmRLmKmASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLAN 114
                                    36     |  46        56       |66|  | |  76        86        96       106        
                                          42-MSE                64-MSE | |                                          
                                                                   67-MSE|                                          
                                                                      70-MSE                                        
                                                                        72-MSE                                      


Chain D from PDB  Type:PROTEIN  Length:88
 aligned with Q8ZPY8_SALTY | Q8ZPY8 from UniProtKB/TrEMBL  Length:114

    Alignment length:88
                                    36        46        56        66        76        86        96       106        
         Q8ZPY8_SALTY    27 QEISKSIYTCNDNQVMEVIYVNTEAGNAYAIISQVNEMIPMRLMKMASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLAN 114
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhh.eeeeeeee.....eeeeeee..eeeeeee......eeeee.......eeeee..eeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3oe3 D  27 QEISKSIYTCNDNQVmEVIYVNTEAGNAYAIISQVNEmIPmRLmKmASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLAN 114
                                    36     |  46        56       |66|  | |  76        86        96       106        
                                          42-MSE                64-MSE | |                                          
                                                                   67-MSE|                                          
                                                                      70-MSE                                        
                                                                        72-MSE                                      


Chain E from PDB  Type:PROTEIN  Length:82
 aligned with Q8ZPY8_SALTY | Q8ZPY8 from UniProtKB/TrEMBL  Length:114

    Alignment length:86
                                    36        46        56        66        76        86        96       106      
         Q8ZPY8_SALTY    27 QEISKSIYTCNDNQVMEVIYVNTEAGNAYAIISQVNEMIPMRLMKMASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSL 112
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhh.eeeeeeee.....eeeeeee..eeeeeee..----.eeee.......eeeee..eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 3oe3 E  27 QEISKSIYTCNDNQVmEVIYVNTEAGNAYAIISQVNEmIPmRLmK----ANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSL 112
                                    36     |  46        56       |66|  ||   76        86        96       106      
                                          42-MSE                64-MSE ||   76                                    
                                                                   67-MSE                                         
                                                                      70-MSE                                      
                                                                       71                                         


Chain F from PDB  Type:PROTEIN  Length:87
 aligned with Q8ZPY8_SALTY | Q8ZPY8 from UniProtKB/TrEMBL  Length:114

    Alignment length:87
                                    37        47        57        67        77        87        97       107       
         Q8ZPY8_SALTY    28 EISKSIYTCNDNQVMEVIYVNTEAGNAYAIISQVNEMIPMRLMKMASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLAN 114
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------MliC-3oe3F01 F:34-110                                                        ---- Pfam domains (1)
           Pfam domains (2) ------MliC-3oe3F02 F:34-110                                                        ---- Pfam domains (2)
           Pfam domains (3) ------MliC-3oe3F03 F:34-110                                                        ---- Pfam domains (3)
           Pfam domains (4) ------MliC-3oe3F04 F:34-110                                                        ---- Pfam domains (4)
           Pfam domains (5) ------MliC-3oe3F05 F:34-110                                                        ---- Pfam domains (5)
           Pfam domains (6) ------MliC-3oe3F06 F:34-110                                                        ---- Pfam domains (6)
         Sec.struct. author .eeeeeeeehhheeeeeeeee.....eeeeeee..eeeeeee......eeeee.......eeeee..eeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3oe3 F  28 EISKSIYTCNDNQVmEVIYVNTEAGNAYAIISQVNEmIPmRLmKmASGANYEAIDKNYTYKLYTKGKTAELVEGDDKPVLSNCSLAN 114
                                    37    |   47        57      | 67  | |   77        87        97       107       
                                         42-MSE                64-MSE | |                                          
                                                                  67-MSE|                                          
                                                                     70-MSE                                        
                                                                       72-MSE
   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 3OE3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OE3)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: MliC] (1)
(-)
Family: MliC (1)
(-)
Salmonella typhimurium (1)
1aMliC-3oe3F01F:34-110
1bMliC-3oe3F02F:34-110
1cMliC-3oe3F03F:34-110
1dMliC-3oe3F04F:34-110
1eMliC-3oe3F05F:34-110
1fMliC-3oe3F06F:34-110

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3OE3)

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  3oe3
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 Related Entries

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(-) Related Entries Specified in the PDB File

3od9