Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF OSPA MUTANT
 
Authors :  K. Makabe, V. Terechko, M. Biancalana, S. Yan, S. Koide
Date :  21 Feb 07  (Deposition) - 04 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  O
Keywords :  Beta-Sheet, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Makabe, M. Biancalana, V. Terechko, S. Yan, G. Gawlak, S. Koide
An Unexpected B-Sheet Register Shift By A Turn Mutation Reveals Opportunistic Nature Of Polypeptide For Maintaining B-Sheet Configuration Through Strand/Strand Interaction
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER SURFACE PROTEIN A
    Chains: O
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 27-273
    Gene: OSPA
    Mutation: YES
    Organism Common: LYME DISEASE SPIROCHETE
    Organism Scientific: BORRELIA BURGDORFERI
    Organism Taxid: 139

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : O

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2OY5)

(-) Sites  (0, 0)

(no "Site" information available for 2OY5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OY5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OY5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 10)

Asymmetric/Biological Unit (10, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_OSPA_BORBU_001 *P35SOSPA_BORBU  ---  ---OP35S
02UniProtVAR_OSPA_BORBU_002 *K39NOSPA_BORBU  ---  ---OK39N
03UniProtVAR_OSPA_BORBU_003 *D59HOSPA_BORBU  ---  ---OD59H
04UniProtVAR_OSPA_BORBU_004 *I90VOSPA_BORBU  ---  ---OI90V
05UniProtVAR_OSPA_BORBU_005 *V114AOSPA_BORBU  ---  ---OV114A
06UniProtVAR_OSPA_BORBU_006 *N127SOSPA_BORBU  ---  ---ON127S
07UniProtVAR_OSPA_BORBU_007 *R144KOSPA_BORBU  ---  ---OR144K
08UniProtVAR_OSPA_BORBU_008 *G149EOSPA_BORBU  ---  ---OG149E
09UniProtVAR_OSPA_BORBU_009 *G164SOSPA_BORBU  ---  ---OG164S
10UniProtVAR_OSPA_BORBU_010 *E196AOSPA_BORBU  ---  ---OE196A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OY5)

(-) Exons   (0, 0)

(no "Exon" information available for 2OY5)

(-) 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 O from PDB  Type:PROTEIN  Length:250
 aligned with OSPA_BORBU | P0CL66 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:252
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
           OSPA_BORBU    22 SSLDEKNSVSVDLPGEMKVLVSKEKNKDGKYDLIATVDKLELKGTSDKNNGSGVLEGVKADKSKVKLTISDDLGQTTLEVFKEDGKTLVSKKVTSKDKSSTEEKFNEKGEVSEKIITRADGTRLEYTGIKSDGSGKAKEVLKGYVLEGTLTAEKTTLVVKEGTVTLSKNISKSGEVSVELNDTDSSAATKKTAAWNSGTSTLTITVNSKKTKDLVFTKENTITVQQYDSNGTKLEGSAVEITKLDEIKNALK 273
               SCOP domains d2o  y5o_ O: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------2oy5O02 O:128-273  [code=3.90.930.1, no name defined]                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...--..eeeeeehhheeeeee........eeeeeee..eeeeeee......eeeeee.....eeeeee.....eeeeeee......eeeeeeee....eeeeee.....eeeeeee.....eeeee.......eeeeee....eeeeee...eeeeeeee..eeeeeeee....eeeeeee........eeeeee....eeeeee..eeeeeeee.....eeeee............ee..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------S---N-------------------H------------------------------V-----------------------A------------S----------------K----E--------------S-------------------------------A----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2oy5 O  24 SHM--KNSVSVDLPGSMKVLVSKSSNADGKYDLIATVDALELSGTSDKNNGSGVLEGVKADASKVKLTISDDLGQTTLEVFKSDGSTLVYKYVYSKDKSYTYEYFNEKGEVSYKYIYRADGTRLEYTGIKSDGSGKAKEVLKGYVLEGTLTAEKTTLVVKEGTVTLSKNISKSGEVSVELNDTDSSAATKKTAAWNSGTSTLTITVNSKKTKDLVFTSSNTITVQQYDSNGTSLEGSAVEITKLDEIKNALK 273
                              |  |  31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
                             26 27                                                                                                                                                                                                                                                      


Chain O from PDB  Type:PROTEIN  Length:250
 aligned with Q45040_BORBG | Q45040 from UniProtKB/TrEMBL  Length:273

    Alignment length:252
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
         Q45040_BORBG    22 SSLDEKNSVSVDLPGEMKVLVSKEKNKDGKYDLIATVDKLELKGTSDKNNGSGVLEGVKADKSKVKLTISDDLGQTTLEVFKEDGKTLVSKKVTSKDKSSTEEKFNEKGEVSEKIITRADGTRLEYTGIKSDGSGKAKEVLKGYVLEGTLTAEKTTLVVKEGTVTLSKNISKSGEVSVELNDTDSSAATKKTAAWNSGTSTLTITVNSKKTKDLVFTKENTITVQQYDSNGTKLEGSAVEITKLDEIKNALK 273
               SCOP domains d2o  y5o_ O: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------2oy5O02 O:128-273  [code=3.90.930.1, no name defined]                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...--..eeeeeehhheeeeee........eeeeeee..eeeeeee......eeeeee.....eeeeee.....eeeeeee......eeeeeeee....eeeeee.....eeeeeee.....eeeee.......eeeeee....eeeeee...eeeeeeee..eeeeeeee....eeeeeee........eeeeee....eeeeee..eeeeeeee.....eeeee............ee..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------S---N-------------------H------------------------------V-----------------------A------------S----------------K----E--------------S-------------------------------A----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2oy5 O  24 SHM--KNSVSVDLPGSMKVLVSKSSNADGKYDLIATVDALELSGTSDKNNGSGVLEGVKADASKVKLTISDDLGQTTLEVFKSDGSTLVYKYVYSKDKSYTYEYFNEKGEVSYKYIYRADGTRLEYTGIKSDGSGKAKEVLKGYVLEGTLTAEKTTLVVKEGTVTLSKNISKSGEVSVELNDTDSSAATKKTAAWNSGTSTLTITVNSKKTKDLVFTSSNTITVQQYDSNGTSLEGSAVEITKLDEIKNALK 273
                              |  |  31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
                             26 27
   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)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OY5)

(-) Gene Ontology  (2, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain O   (Q45040_BORBG | Q45040)
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.

Chain O   (OSPA_BORBU | P0CL66)
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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 2oy5)
 
  Sites
(no "Sites" information available for 2oy5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2oy5)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  2oy5
    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
  OSPA_BORBU | P0CL66
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q45040_BORBG | Q45040
    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
  OSPA_BORBU | P0CL66
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q45040_BORBG | Q45040
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        OSPA_BORBU | P0CL66: 1fj1 1osp 2af5 2fkg 2fkj 2g8c 2hkd 2i5v 2i5z 2ol6 2ol7 2ol8 2oy1 2oy7 2oy8 2oyb 2pi3 3aum 5b10 5b11
        Q45040_BORBG | Q45040: 2fkg 2fkj 2i5v 2i5z 2ol7 2ol8 2oy1 2oy7 2oy8 2oyb 5b2a
UniProtKB/TrEMBL
        Q45040_BORBG | Q45040: 2ol6 2pi3 3cka 3ckf 3ckg 5b3m

(-) Related Entries Specified in the PDB File

2ol6 2ol7 2ol8 2oy1 2oy7 2oy8 2oyb