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(-) Description

Title :  STRUCTURE OF NATIVE RTP34 FROM TREPONEMA PALLIDUM FROM ZINC-SOAKED CRYSTALS
 
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 :  1.90
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
1CL2Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION
4ZN8Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:70 , GLU A:72 , MET A:117 , HIS A:124 , HIS B:155BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:155 , HIS B:70 , GLU B:72 , MET B:117 , HIS B:124BINDING SITE FOR RESIDUE ZN B 302
03AC3SOFTWAREHIS A:149 , HIS B:55 , LYS B:181BINDING SITE FOR RESIDUE ZN B 303
04AC4SOFTWAREASP A:74 , HIS A:76BINDING SITE FOR RESIDUE ZN A 304
05AC5SOFTWAREGLU A:30 , GLU A:72 , ASP A:74 , ASP A:121 , HOH A:572BINDING SITE FOR RESIDUE ZN A 305
06AC6SOFTWAREHIS A:55 , HIS B:149BINDING SITE FOR RESIDUE ZN A 306
07AC7SOFTWAREHIS A:104BINDING SITE FOR RESIDUE ZN A 307
08AC8SOFTWAREHIS A:43 , HIS A:76 , HOH A:608BINDING SITE FOR RESIDUE ZN A 308
09AC9SOFTWAREARG A:165 , TRP A:167 , SER A:168 , GLU A:169 , HOH A:582 , HOH B:512BINDING SITE FOR RESIDUE SO4 A 501
10BC1SOFTWAREGLY B:34 , GLU B:35 , ARG B:37 , TRP B:175 , HOH B:545BINDING SITE FOR RESIDUE SO4 B 502
11BC2SOFTWARESER A:148BINDING SITE FOR RESIDUE CL A 311
12BC3SOFTWAREGLN B:102 , HOH B:562BINDING SITE FOR RESIDUE CL B 312
13BC4SOFTWAREPHE A:31 , PRO A:32 , TYR A:48 , ASP A:68 , LYS A:130 , LYS A:181 , GLN A:184 , HOH A:506BINDING SITE FOR RESIDUE EDO A 401
14BC5SOFTWAREARG A:37 , TRP A:175 , ASP A:176 , HOH A:520 , HOH A:571BINDING SITE FOR RESIDUE EDO A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O6E)

(-) 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 2O6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O6E)

(-) Exons   (0, 0)

(no "Exon" information available for 2O6E)

(-) 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.......eee...............eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6e A  28 FDEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDEYSLHIDEQTGVSGRFWSEPLVAEWDDFEWKGPQW 185
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177        


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 (1) Iron_transport-2o6eB01 B:29-182                                                                                                                           --- Pfam domains (1)
           Pfam domains (2) Iron_transport-2o6eB02 B:29-182                                                                                                                           --- Pfam domains (2)
         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
                 2o6e B  29 DEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDEYSLHIDEQTGVSGRFWSEPLVAEWDDFEWKGPQW 185
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178
   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 2O6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O6E)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Iron_transport] (3)

(-) 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

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        TA34_TREPA | P19478: 2o6c 2o6d 2o6f 3pjl 3pjn

(-) Related Entries Specified in the PDB File

2o6c 2o6d 2o6f