Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF A PUTATIVE RIBOSOME-BINDING FACTOR FROM MYCOPLASMA PNEUMONIAE (MPN156)
 
Authors :  S. M. Rubin, J. G. Pelton, H. Yokota, R. Kim, D. E. Wemmer, Berkeley Structural Genomics Center (Bsgc)
Date :  13 May 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (16x)
Keywords :  Ribosome-Binding Factor, Structural Genomics, Distant Homology, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Rubin, J. G. Pelton, H. Yokota, R. Kim, D. E. Wemmer
Solution Structure Of A Putative Ribosome Binding Protein From Mycoplasma Pneumoniae And Comparison To A Distant Homolog.
J. Struct. Funct. Genom. V. 4 235 2003
PubMed-ID: 15185964  |  Reference-DOI: 10.1023/B:JSFG.0000016127.57320.82
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE RIBOSOME-BINDING FACTOR A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSKB3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MPN156
    Organism Scientific: MYCOPLASMA PNEUMONIAE
    Organism Taxid: 2104

 Structural Features

(-) Chains, Units

  
NMR Structure (16x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PA4)

(-) Sites  (0, 0)

(no "Site" information available for 1PA4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PA4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PA4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PA4)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RBFAPS01319 Ribosome-binding factor A signature.RBFA_MYCPN73-94  1A:73-94

(-) Exons   (0, 0)

(no "Exon" information available for 1PA4)

(-) Sequences/Alignments

NMR Structure
   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:96
 aligned with RBFA_MYCPN | P75589 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:96
                                    15        25        35        45        55        65        75        85        95      
           RBFA_MYCPN     6 KERLENDIIRLINRTVIHEIYNETVKTGHVTHVKLSDDLLHVTVYLDCYNREQIDRVVGAFNQAKGVFSRVLAHNLYLAKAVQIHFVKDKAIDNAM 101
               SCOP domains d1pa4a_ A: Ribosome-binding factor A, RbfA                                                       SCOP domains
               CATH domains 1pa4A00 A:6-101  [code=3.30.300.20, no name defined]                                             CATH domains
               Pfam domains RBFA-1pa4A01 A:6-101                                                                             Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.......hhh.eeeeeeee....eeeeeee......hhhhhhhhhh.hhhhhhhhhhh.......eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------RBFA  PDB: A:73-94    ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1pa4 A   6 KERLENDIIRLINRTVIHEIYNETVKTGHVTHVKLSDDLLHVTVYLDCYNREQIDRVVGAFNQAKGVFSRVLAHNLYLAKAVQIHFVKDKAIDNAM 101
                                    15        25        35        45        55        65        75        85        95
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: RBFA] (3)

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A   (RBFA_MYCPN | P75589)
biological process
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1pa4)
 
  Sites
(no "Sites" information available for 1pa4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pa4)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pa4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RBFA_MYCPN | P75589
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RBFA_MYCPN | P75589
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1PA4)

(-) Related Entries Specified in the PDB File

5796 RESONANCE ASSIGNMENTS FOR MPN156
1kkg RIBOSOME-BINDING FACTOR A FROM E. COLI RELATED ID: BSGCAIR30410 RELATED DB: TARGETDB