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(-) Description

Title :  STRUCTURE OF SELENOMETHIONYL RTP34 FROM TREPONEMA PALLIDUM
 
Authors :  M. Machius, C. A. Brautigam, R. K. Deka, D. R. Tomchick, S. B. Lumpkins, M. V. Norgard
Date :  07 Dec 06  (Deposition) - 26 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ig-Fold, Syphilis, Metal-Ion Binding, Dimer, Membrane Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Deka, C. A. Brautigam, F. L. Tomson, S. B. Lumpkins, D. R. Tomchick M. Machius, M. V. Norgard
Crystal Structure Of The Tp34 (Tp0971) Lipoprotein Of Treponema Pallidum: Implications Of Its Metal-Bound State And Affinity For Human Lactoferrin.
J. Biol. Chem. V. 282 5944 2007
PubMed-ID: 17192261  |  Reference-DOI: 10.1074/JBC.M610215200

(-) Compounds

Molecule 1 - 34 KDA MEMBRANE ANTIGEN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEXHTA
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TPD
    Mutation: YES
    Organism Scientific: TREPONEMA PALLIDUM
    Organism Taxid: 160
    Synonym: PATHOGEN-SPECIFIC MEMBRANE ANTIGEN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:165 , TRP A:167 , SER A:168 , GLU A:169 , HOH A:450 , HOH B:514 , HOH B:552BINDING SITE FOR RESIDUE SO4 B 501
2AC2SOFTWAREGLY B:34 , GLU B:35 , ARG B:37 , TRP B:175 , HOH B:580BINDING SITE FOR RESIDUE SO4 B 502
3AC3SOFTWAREHIS A:149BINDING SITE FOR RESIDUE CL A 301
4AC4SOFTWAREARG A:141BINDING SITE FOR RESIDUE CL A 302
5AC5SOFTWAREHOH A:514BINDING SITE FOR RESIDUE CL A 304
6AC6SOFTWAREPHE A:31 , PRO A:32 , TYR A:48 , ASP A:68 , LYS A:130 , LYS A:181 , GLN A:184 , HOH A:408BINDING SITE FOR RESIDUE EDO A 401
7AC7SOFTWAREARG A:37 , TRP A:175 , ASP A:176 , HOH A:425 , HOH A:506 , HOH A:533BINDING SITE FOR RESIDUE EDO A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O6C)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:55 -Pro A:56
2His B:55 -Pro B:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O6C)

(-) Exons   (0, 0)

(no "Exon" information available for 2O6C)

(-) Sequences/Alignments

Asymmetric/Biological 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:158
 aligned with TA34_TREPA | P19478 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:158
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196        
           TA34_TREPA    47 FDEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDEYSLHIDEQTGVSGRFWSEPLVAEWDDFEWKGPQW 204
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eee..eeeeeeee....ee.............eeeeeeeee.hhhhhhh..........eeeeeeee......eeee.eeeee..eeeeeeee......eeeeeeeeee..hhhhheee...............eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6c A  28 FDEFPIGEDRDVGPLHVGGVYFQPVEmHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVmFAPmNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDEYSLHIDEQTGVSGRFWSEPLVAEWDDFEWKGPQW 185
                                    37        47      | 57        67        77        87        97       107     | 117       127       137       147       157       167       177        
                                                     54-MSE                                                    113-MSE                                                                    
                                                                                                                   117-MSE                                                                


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with TA34_TREPA | P19478 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:157
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       
           TA34_TREPA    48 DEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDEYSLHIDEQTGVSGRFWSEPLVAEWDDFEWKGPQW 204
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eee..eeeeeeee....ee.............eeeeeeeee.hhhhhhh..........eeeeeeee......eeee.eeeee..eeeeeeee......eeeeeeeeee.......eee...............eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6c B  29 DEFPIGEDRDVGPLHVGGVYFQPVEmHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVmFAPmNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDEYSLHIDEQTGVSGRFWSEPLVAEWDDFEWKGPQW 185
                                    38        48     |  58        68        78        88        98       108    |  118       128       138       148       158       168       178       
                                                    54-MSE                                                    113-MSE                                                                    
                                                                                                                  117-MSE
   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 2O6C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O6C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O6C)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TA34_TREPA | P19478)
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TA34_TREPA | P19478: 2o6d 2o6e 2o6f 3pjl 3pjn

(-) Related Entries Specified in the PDB File

2o6d 2o6e 2o6f