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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SINGLE-STRANDED DNA-BINDING PROTEIN FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  K. Saikrishnan, G. P. Manjunath, P. Singh, J. Jeyakanthan, Z. Dauter, K K. Muniyappa, M. Vijayan
Date :  05 May 05  (Deposition) - 15 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oligonucleotide Binding Fold, Dna-Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Saikrishnan, G. P. Manjunath, P. Singh, J. Jeyakanthan, Z. Dauter, K. Sekar, K. Muniyappa, M. Vijayan
Structure Of Mycobacterium Smegmatis Single-Stranded Dna-Binding Protein And A Comparative Study Involving Homologus Ssbs: Biological Implications Of Structural Plasticity And Variability In Quaternary Association.
Acta Crystallogr. , Sect. D V. 61 1140 2005
PubMed-ID: 16041080  |  Reference-DOI: 10.1107/S0907444905016896
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SINGLE-STRAND BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Synonym: SINGLE-STRANDED DNA-BINDING PROTEIN, SSB, HELIX- DESTABILIZING PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:100 , HOH A:1011 , HOH A:1012 , GLU B:65BINDING SITE FOR RESIDUE CD B 1001
2AC2SOFTWAREGLU A:51 , HOH A:1016 , HOH A:1017 , GLU B:69BINDING SITE FOR RESIDUE CD A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X3F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X3F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X3F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X3F)

(-) Exons   (0, 0)

(no "Exon" information available for 1X3F)

(-) 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:107
 aligned with SSB_MYCS2 | Q9AFI5 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
            SSB_MYCS2     3 GDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d1x3fa_ A: automated matches                                                                                           SCOP domains
               CATH domains 1x3fA00 A:3-120 Nucleic acid-binding            proteins                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eeee.....eeeeeeeee...-----------...eeeeeeeehhhhhhhhhhh....eeeeeeeeeeeee.......eeeeeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1x3f A   3 GDTTITVVGNLTADPELRFTPSGAAVANFTVASTPR-----------GEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    12        22        32     |   -       |52        62        72        82        92       102       112        
                                                              38          50                                                                      


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with SSB_MYCS2 | Q9AFI5 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
            SSB_MYCS2     2 AGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKAS 121
               SCOP domains d1x3fb_ B: automated matches                                                                                             SCOP domains
               CATH domains 1x3fB00 B:2-121 Nucleic acid-binding proteins                                                                            CATH domains
           Pfam domains (1) --SSB-1x3fB01 B:4-109                                                                                       ------------ Pfam domains (1)
           Pfam domains (2) --SSB-1x3fB02 B:4-109                                                                                       ------------ Pfam domains (2)
         Sec.struct. author ....eeeeeeee....eeee.....eeeeeeee...ee........ee....eeeeeeehhhhhhhhhhh....eeeeeeeeeeeee.-----.eeeeeeeeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1x3f B   2 AGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFE-----KRTVVEVEVDEIGPSLRYATAKVNKAS 121
                                    11        21        31        41        51        61        71        81       | -   |   101       111       121
                                                                                                                  89    95
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  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 beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SSB_MYCS2 | Q9AFI5)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SSB_MYCS2 | Q9AFI5: 1x3e 1x3g 3a5u

(-) Related Entries Specified in the PDB File

1x3e THE SAME PROTEIN AT 2.15 ANGSTROM
1x3g THE SAME PROTEIN AT 3.00 ANGSTROM