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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN FROM MYCOBACTERIUM LEPRAE (FORM I)
 
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 :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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
    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

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:54 , LEU B:55 , ARG B:56 , GLN B:85 , VAL B:99 , HOH B:258BINDING SITE FOR RESIDUE GOL B 169
2AC2SOFTWAREGLU A:100 , GLU B:62 , GLU B:65 , HOH B:217BINDING SITE FOR RESIDUE CD B 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AFP)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:109
 aligned with SSB_MYCLE | P46390 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
            SSB_MYCLE     3 GDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRIYDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d3afpa_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......ee.....eeeeeeeee..--------.......eeeeeeeehhhhhhhhhhh....eeeeeeeeeeeee.-.....eeeeeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3afp A   3 GDTTITIVGNLTADPELRFTSSGAAVVNFTVASTP--------EWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRSFE-REGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    12        22        32    |    -   |    52        62        72        82      | 92       102       112        
                                                             37       46                                         89 |                             
                                                                                                                   91                             


Chain B from PDB  Type:PROTEIN  Length:115
 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 d3afpb_ B: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee....eeee.....eeeeeeeee....---..........eeeeeeeehhhhhhhhhhh....eeeeeeeeeee.-.........eeeeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3afp B   2 AGDTTITIVGNLTADPELRFTSSGAAVVNFTVASTPRI---QSGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVTGRLKQRS-ETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31       | - |      51        61        71        81     | |91       101       111         
                                                                39  43                                          87 |                               
                                                                                                                  89
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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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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

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 Related Entries

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

UniProtKB/Swiss-Prot
        SSB_MYCLE | P46390: 3afq

(-) Related Entries Specified in the PDB File

3afq