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 :  CRYSTAL STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN FROM MYCOBACTERIUM LEPRAE (FORM II)
 
Authors :  P. S. Kaushal, P. Singh, A. Sharma, K. Muniyappa, M. Vijayan
Date :  10 Mar 10  (Deposition) - 06 Oct 10  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ob-Fold, Quaternary Structure And Stability, Changes On Oligomerisation, Water-Bridges, Dna Damage, Dna Repair, Dna Replication, Dna-Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Kaushal, P. Singh, A. Sharma, K. Muniyappa, M. Vijayan
X-Ray And Molecular-Dynamics Studies On Mycobacterium Lepra Single-Stranded Dna-Binding Protein And Comparison With Other Eubacterial Ssb Structures
Acta Crystallogr. , Sect. D V. 66 1048 2010
PubMed-ID: 20944238  |  Reference-DOI: 10.1107/S0907444910032208
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SINGLE-STRANDED DNA-BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A, PMLSSB
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SSB
    Organism Scientific: MYCOBACTERIUM LEPRAE
    Organism Taxid: 272631
    Strain: TN
    Synonym: SSB, HELIX-DESTABILIZING PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3AFQ)

(-) Sites  (0, 0)

(no "Site" information available for 3AFQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AFQ)

(-) 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:105
 aligned with SSB_MYCLE | P46390 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            SSB_MYCLE     2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d3afqa_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..............eeeeeeee..----------.....eeeeeeeehhhhhhhhhhh....eeeeeeeeeeee....----.eeeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3afq A   2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTP----------KDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFETR----RTVVEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31     |   -      | 51        61        71        81        91    |  101       111         
                                                              37         48                                         91   96                        


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with SSB_MYCLE | P46390 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            SSB_MYCLE     2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d3afqb_ B: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee....eee.......eeeeeeee....ee.--.ee.....eeeeeeeehhhhhhhhhhh....eeeeeeeeeeeee----...eeeeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3afq B   2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDR--GEWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSF----GEKRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31        41|  |    51        61        71        81      |  - |     101       111         
                                                                   42 45                                         88   93                           


Chain C from PDB  Type:PROTEIN  Length:105
 aligned with SSB_MYCLE | P46390 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            SSB_MYCLE     2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d3afqc_ C: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeee.....eeeeeeeee...-------.......eeeeeeeehhhhhhhhhhh....eeeeeeeeeee.-------...eeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3afq C   2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPR-------EWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRS-------KRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31      |  -    |   51        61        71        81     |   -   |   101       111         
                                                               38      46                                       87      95                         


Chain D from PDB  Type:PROTEIN  Length:107
 aligned with SSB_MYCLE | P46390 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            SSB_MYCLE     2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d3afqd_ D: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eee.......eeeeeeee......-----......eeeeeeeehhhhhhhhhhh....eeeeeeeeeee...-------.eeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3afq D   2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYD-----WKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFE-------TVVEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31        41     |  51        61        71        81       | -     | 101       111         
                                                                  41    47                                        89      97
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AFQ)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SSB_MYCLE | P46390)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

 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 3afq)
 
  Sites
(no "Sites" information available for 3afq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3afq)
 

(-) 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
  3afq
    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
  SSB_MYCLE | P46390
    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
  SSB_MYCLE | P46390
    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
        SSB_MYCLE | P46390: 3afp

(-) Related Entries Specified in the PDB File

3afp