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(-) Description

Title :  CRYSTAL STRUCTURE OF TREPONEMA PALLIDUM PROTEIN TP0624
 
Authors :  M. L. Parker, M. J. Boulanger
Date :  22 Apr 16  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Ompa-Like, Peptidoglycan, Modular Assembly, Neofunctionalized, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Parker, S. Houston, C. Wetherell, C. E. Cameron, M. J. Boulanger
The Structure Of Treponema Pallidum Tp0624 Reveals A Modula Assembly Of Divergently Functionalized And Previously Uncharacterized Domains.
Plos One V. 11 66274 2016
PubMed-ID: 27832149  |  Reference-DOI: 10.1371/JOURNAL.PONE.0166274

(-) Compounds

Molecule 1 - OOP FAMILY OMPA-OMPF PORIN
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TP_0624, TPANIC_0624
    Organism Scientific: TREPONEMA PALLIDUM (STRAIN NICHOLS)
    Organism Taxid: 243276
    Strain: NICHOLS
    Synonym: UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x):  B
Biological Unit 2 (1x): A 
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN B:124 , ASN B:125 , HIS B:133 , TYR B:339 , HIS B:340 , HOH B:616 , HOH B:637 , HOH B:680binding site for residue GOL B 501
02AC2SOFTWAREARG B:105 , VAL B:152binding site for residue CL B 502
03AC3SOFTWAREALA B:410 , ARG B:425 , ARG B:467binding site for residue CL B 503
04AC4SOFTWARESER B:123 , GLN B:124 , GLN B:283binding site for residue CL B 504
05AC5SOFTWAREGLN A:427 , PRO B:415 , GLN B:416 , HOH B:755binding site for residue CL B 505
06AC6SOFTWARELEU B:93 , HOH B:690binding site for residue CL B 506
07AC7SOFTWAREASP A:122 , LYS A:135 , PHE A:177 , PHE A:225 , LYS A:239 , HOH A:671binding site for residue GOL A 501
08AC8SOFTWAREHIS A:212 , GLU A:214 , PHE A:281 , GLY A:282 , GLN A:283 , ARG A:357binding site for residue GOL A 502
09AC9SOFTWARECYS A:223 , LEU A:224 , GLY A:251 , VAL A:253 , TYR A:255 , HOH A:624 , HOH A:634 , HOH A:645binding site for residue GOL A 503
10AD1SOFTWAREALA A:410 , ARG A:425 , ARG A:467binding site for residue CL A 504
11AD2SOFTWARELEU A:93 , ARG A:160binding site for residue CL A 505
12AD3SOFTWAREPRO A:415 , GLN A:416 , GLN B:427binding site for residue CL A 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JIR)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu B:93 -Pro B:94
2Tyr B:328 -Pro B:329
3Leu A:93 -Pro A:94
4Tyr A:328 -Pro A:329

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JIR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JIR)

(-) Exons   (0, 0)

(no "Exon" information available for 5JIR)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhhheeeee.......eeeeeeeeehhhhhhhhh......................eeee....ee......ee.........eee....eeehhhhhhhhhhhhhh..eee...hhhhhhhhhh...eeee..eee.....eeeehhhhhhhhhhhhhhhhhhhhh.eeee.hhhhheee......hhhhhhhhhhhhhhhhhhh...eeeee....eeeeee...........hhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee...........hhhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jir A  64 AVHTDAVQDWKNGTINAQLTLDLARARMRLPADRTAASQFLRYKAPAQLKDVYLSVLVDSQNRVGDCLAHEKIRLADITALVDAGHHAVTTLSPSVRSLQLSHQTPLTALARLFVTHETAYVPAIPPTSAVSRPYTGILIDARGSLPVHGEYVSEPLSACLFPKIWSTDMDLIYEKNMVHPDRAKAWGVVRYGSVWDEKMYRDRIGTTPLKIIARGVFGQQRTDPIIASKDAAQILARPENLRLLAEGNVIILCDEAALRVHVPYPLVDEHFYFAYHDVKRFLTDERSPGVGVRSGINTLKITVYDVRFVANSPEILASEKDRVDVIATALKKMGPYTRFLIEGHTADLHRPQEEAALSVARAQRMAQELSRRGIEMTRITTAGHGATKPIAPSDTHANKAKNRRVEITILRD 476
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473   


Chain B from PDB  Type:PROTEIN  Length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh...hhhhhhh........ee.......eeeeeeeeehhhhhhhhh............eeeee....ee......ee.........eee....eeehhhhhhhhhhhhhh..eeehhhhh..hhhhhh..eeeee..eee.....eeeehhhhhhhhhhhhhhhhhhhhh.eeee.hhhhheee......hhhhhhhhhhhhhhhhhhh...eeeee....eeeeee...........hhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee...........hhhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jir B  63 DAVHTDAVQDWKNGTINAQLTLDLARARMRLPADRTAASQFLRYKAPAQLKDVYLSVLVDSQNRVGDCLAHEKIRLADITALVDAGHHAVTTLSPSVRSLQLSHQTPLTALARLFVTHETAYVSRPYTGILIDARGSLPVHGEYVSEPLSACLFPKIWSTDMDLIYEKNMVHPDRAKAWGVVRYGSVWDEKMYRDRIGTTPLKIIARGVFGQQRTDPIIASKDAAQILARPENLRLLAEGNVIILCDEAALRVHVPYPLVDEHFYFAYHDVKRFLTDERSPGVGVRSGINTLKITVYDVRFVANSPEILASEKDRVDVIATALKKMGPYTRFLIEGHTADLHRPQEEAALSVARAQRMAQELSRRGIEMTRITTAGHGATKPIAPSDTHANKAKNRRVEITILRD 476
                                    72        82        92       102       112       122       132       142       152       162       172       182  ||   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471     
                                                                                                                                                    185|                                                                                                                                                                                                                                                                                         
                                                                                                                                                     195
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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 5JIR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JIR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JIR)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5JIR)

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5jk2