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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF TRWG TYPE IV SECRETION MACHINERY FROM BARTONELLA GRAHAMII
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  04 Nov 13  (Deposition) - 05 Mar 14  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Host-Specific Interaction, Outer Membrane Protein, Pathogenesis, Type Iv Secretion System, Virb8, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Gillespie, I. Q. Phan, H. Scheib, S. Subramanian, T. E. Edwards, S. S. Lehman, H. Piitulainen, M. S. Rahman, K. E. Rennoll-Bankert, B. L. Staker, S. Taira, R. Stacy, P. J. Myler, A. F. Azad, A. T. Pulliaine
Structural Insight Into How Bacteria Prevent Interference Between Multiple Divergent Type Iv Secretion Systems.
Mbio V. 6 01867 2015
PubMed-ID: 26646013  |  Reference-DOI: 10.1128/MBIO.01867-15

(-) Compounds

Molecule 1 - TRWG PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: BG1861
    Fragment: SOLUBLE DOMAIN (UNP RESIDUES 63-233)
    Gene: BGR_19310, TRWG
    Organism Scientific: BARTONELLA GRAHAMII
    Organism Taxid: 634504
    Strain: AS4AUP

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:115 , HOH A:406 , ASP B:113 , ASP B:115 , HOH B:428 , HOH B:481BINDING SITE FOR RESIDUE CA B 301
2AC2SOFTWAREASP C:113 , ASP C:115 , HOH C:446 , ASP D:115 , HOH D:382 , HOH D:395BINDING SITE FOR RESIDUE CA C 301
3AC3SOFTWARESER E:182 , HOH E:409 , ASP F:226 , HOH F:410 , HOH F:471 , HOH F:472BINDING SITE FOR RESIDUE CA E 301
4AC4SOFTWAREASP E:115 , HOH E:447 , ASP F:113 , ASP F:115 , HOH F:417 , HOH F:469BINDING SITE FOR RESIDUE CA F 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NHF)

(-) 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:144
                                                                                                                                                                                
               SCOP domains d4nhfa_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhh...eeeeeeeeeee....eeeeeeeeeee..........eeeeeeeeeee.....hhhhhhhh...eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nhf A  89 HETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDPEILLN 232
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228    


Chain B from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains d4nhfb_ B: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhh...eeeeeeeeeee....eeeeeeeeeee.......eeeeeeeeeee.....hhhhhhhh...eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nhf B  92 SYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSTTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDPEILLN 232
                                   101       111       121       131       141       151       161       171       181||     194       204       214       224        
                                                                                                                    182|                                              
                                                                                                                     186                                              


Chain C from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains d4nhfc_ C: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhh......hhhhhhh...eeeeeeeeeee....eeeeeeeeeee..........eeeeeeeeeee.....hhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhf C  90 ETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDPEILL 231
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229  


Chain D from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains d4nhfd_ D: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhh..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeee.....hhhhhh.....eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhf D  90 ETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDPEILL 231
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229  


Chain E from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains d4nhfe_ E: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhh..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeee.....hhhhhhhh...eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhf E  90 ETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDPEILL 231
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229  


Chain F from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains d4nhff_ F: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhh...eeeeeeeeeee....eeeeeeeeeee..........eeeeeeeeeee.....hhhhhhhh...eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nhf F  90 ETSYGEVVDRYWLNQYVLNRENYDYDTIQLNYDTTALLSAASVQQEYYKIYDGENARDKVLSNKARITVKVRSIQLNGLGQATVRFTTQQLDSSGATTGPKQHQIATIGYTYVGAPMKSSDRLLNPLGFQITSYRSDPEILLN 232
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229
   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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4NHF)

(-) Related Entries Specified in the PDB File

4jf8 TRWG FROM BARTONELLA BIRTLESII
4kz1 VIRB8 FROM BARTONELLA GRAHAMII
4lso VIRB8 FROM BARTONELLA QUINTANA
4mei VIRB8 FROM BARTONELLA TRIBOCORUM RELATED ID: SSGCID-372648 RELATED DB: TARGETTRACK