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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PED208 TRAM N-TERMINAL DOMAIN
 
Authors :  J. J. W. Wong, J. Lu, R. A. Edwards, L. S. Frost, J. N. Mark Glover
Date :  27 Aug 10  (Deposition) - 25 May 11  (Release) - 07 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Dna Binding Protein, Dimer, Bacterial Conjugation, Ribbon-Helix- Helix, Transcriptional Repressor, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Wong, J. Lu, R. A. Edwards, L. S. Frost, J. N. Glover
Structural Basis Of Cooperative Dna Recognition By The Plasmid Conjugation Factor, Tram.
Nucleic Acids Res. V. 39 6775 2011
PubMed-ID: 21565799  |  Reference-DOI: 10.1093/NAR/GKR296

(-) Compounds

Molecule 1 - PROTEIN TRAM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1-52
    Gene: TRAM
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:18 , THR A:21 , HOH A:88 , GLY B:27 , ILE B:28 , GLU B:29 , GLU B:30 , HOH B:106 , HOH B:162BINDING SITE FOR RESIDUE GOL A 53
2AC2SOFTWAREALA B:31 , ASN B:35 , HOH B:61 , HOH B:78BINDING SITE FOR RESIDUE MG B 53

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OMY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OMY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OMY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OMY)

(-) Exons   (0, 0)

(no "Exon" information available for 3OMY)

(-) 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:51
 aligned with TRAM8_ECOLX | P33788 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:51
                                    11        21        31        41        51 
           TRAM8_ECOLX    2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQ 52
               SCOP domains d3omya_ A: automated matches                        SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  3omy A  2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQQ 52
                                    11        21        31        41        51 


Chain B from PDB  Type:PROTEIN  Length:50
 aligned with TRAM8_ECOLX | P33788 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:50
                                    11        21        31        41        51
           TRAM8_ECOLX    2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQ 51
               SCOP domains d3omyb_ B: automated matches                       SCOP domains
               CATH domains -------------------------------------------------- CATH domains
           Pfam domains (1) Tra_M-3omyB01 B:2-51                               Pfam domains (1)
           Pfam domains (2) Tra_M-3omyB02 B:2-51                               Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  3omy B  2 PKIQTYVNNNVYEQITDLVTIRKQEGIEEASLSNVSSMLLELGLRVYMIQ 51
                                    11        21        31        41        51
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OMY)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Tra_M] (2)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRAM8_ECOLX | P33788)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRAM8_ECOLX | P33788: 3on0

(-) Related Entries Specified in the PDB File

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