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(-) Description

Title :  B-REPEAT OF LISTERIA MONOCYTOGENES INLB (INTERNALIN B)
 
Authors :  M. Ebbes, H. H. Niemann
Date :  17 Jan 11  (Deposition) - 23 Feb 11  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B,C,D  (1x)
Keywords :  Protein Binding, Virulence Factor, Pathogenicity Factor, Beta-Grasp Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ebbes, W. M. Bleymuller, M. Cernescu, R. Nolker, B. Brutschy, H. H. Niemann
Fold And Function Of The Inlb B-Repeat.
J. Biol. Chem. V. 286 15496 2011
PubMed-ID: 21345802  |  Reference-DOI: 10.1074/JBC.M110.189951

(-) Compounds

Molecule 1 - INTERNALIN B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: CODON PLUS
    Expression System Vector: PETM30
    Expression System Vector Type: PLASMID
    Fragment: B-REPEAT, RESIDUES 322-392
    Organism Scientific: LISTERIA MONOCYTOGENES EGD
    Organism Taxid: 1334565
    Synonym: INLB

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:363 , ASN A:365 , HOH A:2052 , HOH A:2092BINDING SITE FOR RESIDUE CA A1393
02AC2SOFTWAREASP A:330 , LYS A:358 , LYS A:389 , HOH A:2088BINDING SITE FOR RESIDUE CA A1394
03AC3SOFTWARELYS B:358 , GLU B:369 , HOH B:2048 , HOH B:2052 , HOH B:2073 , HOH B:2092BINDING SITE FOR RESIDUE CA B1393
04AC4SOFTWAREHOH B:2067 , HOH B:2074 , HOH B:2078 , HOH B:2079 , HOH B:2081 , HOH C:2109 , HOH C:2128BINDING SITE FOR RESIDUE CA B1394
05AC5SOFTWAREASP C:381 , HOH C:2104 , HOH C:2105 , HOH C:2113 , HOH C:2114 , HOH C:2129 , HOH C:2130BINDING SITE FOR RESIDUE CA C1393
06AC6SOFTWARETHR C:342 , ARG C:343 , HOH C:2032 , HOH C:2069BINDING SITE FOR RESIDUE CL C1394
07AC7SOFTWAREASN C:380 , ASP C:381 , ALA C:390BINDING SITE FOR RESIDUE CL C1395
08AC8SOFTWAREHOH B:2019 , GLU C:391 , HOH C:2125 , HOH C:2126 , HOH C:2127BINDING SITE FOR RESIDUE CA C1396
09AC9SOFTWAREHOH B:2090 , HOH C:2077 , HOH C:2098 , HOH C:2100 , HOH C:2101BINDING SITE FOR RESIDUE CA C1397
10BC1SOFTWARELYS D:389 , ALA D:390BINDING SITE FOR RESIDUE CL D1392
11BC2SOFTWAREHOH B:2027 , ASP D:330 , HOH D:2008BINDING SITE FOR RESIDUE CA D1393

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y5P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y5P)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y5P)

(-) 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:72
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:72
                                   330       340       350       360       370       380       390  
           INLB_LISMO   321 EVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET 392
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...........ee..eeeeeee....................eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2y5p A 321 MVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET 392
                                   330       340       350       360       370       380       390  


Chain B from PDB  Type:PROTEIN  Length:72
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:72
                                   330       340       350       360       370       380       390  
           INLB_LISMO   321 EVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET 392
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee................eeeeee....................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2y5p B 321 MVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET 392
                                   330       340       350       360       370       380       390  


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:73
                                   329       339       349       359       369       379       389   
           INLB_LISMO   320 KEVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET 392
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee...........ee..eeeeeee....................eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 2y5p C 320 AMVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET 392
                                   329       339       349       359       369       379       389   


Chain D from PDB  Type:PROTEIN  Length:72
 aligned with INLB_LISMO | P25147 from UniProtKB/Swiss-Prot  Length:630

    Alignment length:72
                                   329       339       349       359       369       379       389  
           INLB_LISMO   320 KEVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAE 391
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------Flg_new-2y5pD01 D:350-391                  Pfam domains (1)
           Pfam domains (2) ------------------------------Flg_new-2y5pD02 D:350-391                  Pfam domains (2)
           Pfam domains (3) ------------------------------Flg_new-2y5pD03 D:350-391                  Pfam domains (3)
           Pfam domains (4) ------------------------------Flg_new-2y5pD04 D:350-391                  Pfam domains (4)
         Sec.struct. author ..eeeeeeee..eeeeeeee...............eeeeeeeee..eeee............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 2y5p D 320 AMVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAE 391
                                   329       339       349       359       369       379       389
   Legend:   → Mismatch (orange background)
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  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 2Y5P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y5P)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Flg_new] (1)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (INLB_LISMO | P25147)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        INLB_LISMO | P25147: 1d0b 1h6t 1m9s 1otm 1otn 1oto 2uzx 2uzy 2wqu 2wqv 2wqw 2wqx 2y5q 4aw4 4cil

(-) Related Entries Specified in the PDB File

1d0b INTERNALIN B LEUCINE RICH REPEAT DOMAIN
1h6t INTERNALIN B: CRYSTAL STRUCTURE OF FUSED N-TERMINAL DOMAINS.
1m9s CRYSTAL STRUCTURE OF INTERNALIN B (INLB), A LISTERIAMONOCYTOGENES VIRULENCE PROTEIN CONTAINING SH3-LIKE DOMAINS.
1otm CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1otn CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
1oto CALCIUM-BINDING MUTANT OF THE INTERNALIN B LRR DOMAIN
2uzx STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: CRYSTAL FORM I
2uzy STRUCTURE OF THE HUMAN RECEPTOR TYROSINE KINASE MET IN COMPLEX WITH THE LISTERIA MONOCYTOGENES INVASION PROTEIN INLB: LOW RESOLUTION, CRYSTAL FORM II
2wqu INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: TRICLINIC CRYSTAL FORM
2wqv INTERNALIN DOMAIN OF LISTERIA MONOCYTOGENES INLB: RHOMBOHEDRAL CRYSTAL FORM
2wqw DOUBLE-DISULFIDE CROSS-LINKED CRYSTAL DIMER OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN
2wqx INLB321_4R: S199R, D200R, G206R, A227R, C242A MUTANT OF THE LISTERIA MONOCYTOGENES INLB INTERNALIN DOMAIN
2y5q LISTERIA MONOCYTOGENES INLB (INTERNALIN B) RESIDUES 36-392