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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. Sekar, K. Muniyappa, M. Vijayan

Date :   05 May 05 (Deposition) - 15 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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)

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CD	1	Ligand/Ion	CADMIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:56 , GLU A:100 , GLU B:62 , GLU B:65	BINDING SITE FOR RESIDUE CD A 1001

(no "SS Bond" information available for 1X3G)

(no "Cis Peptide Bond" information available for 1X3G)

(no "SAP(SNP)/Variant" information available for 1X3G)

(no "PROSITE Motif" information available for 1X3G)

(no "Exon" information available for 1X3G)

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
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Chain A from PDB  Type:PROTEIN  Length:114
 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 d1x3ga_ A: automated matches                                                                                           SCOP domains
               CATH domains 1x3gA00 A:3-120 Nucleic acid-binding pro    teins                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......ee.....eeeeeeeee.......----......eeeeeeeehhhhhhhhhhh....eeeeeeeeeee...........eeeeeeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1x3g A   3 GDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDR----WKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    12        22        32        42    |   52        62        72        82        92       102       112        
                                                                  42   47

Chain B from PDB  Type:PROTEIN  Length:115
 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 d1x3gb_ B: automated matches                                                                                           SCOP domains
               CATH domains 1x3gB00 B:3-120 Nucleic acid-binding proteins                                                                          CATH domains
           Pfam domains (1) -SSB-1x3gB01 B:4-109                                                                                       ----------- Pfam domains (1)
           Pfam domains (2) -SSB-1x3gB02 B:4-109                                                                                       ----------- Pfam domains (2)
         Sec.struct. author ...eeeeeeee....eeee.....eeeeeeee...................eeeeeeehhhhhhhhhhh....eeeeeeeeeeee....---..eeeeeeeeeeee.......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1x3g B   3 GDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETR---KRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    12        22        32        42        52        62        72        82        |-  |    102       112        
                                                                                                                   91  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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Single strand DNA-binding domain, SSB (96)

Protein domain: automated matches (30)

Mycobacterium smegmatis [TaxId: 1772] (3)

1a	d1x3ga_	A:
1b	d1x3gb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

Mycobacterium smegmatis. Organism_taxid: 1772. (3)

1a	1x3gA00	A:3-120
1b	1x3gB00	B:3-120

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: OB (224)

Family: SSB (18)

Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (3)

1a	SSB-1x3gB01	B:4-109
1b	SSB-1x3gB02	B:4-109

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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Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	SSB_MYCS2 \| Q9AFI5	:	1x3e 1x3f 3a5u

1x3e	THE SAME PROTEIN AT 2.15 ANGSTROM
1x3f	THE SAME PROTEIN AT 2.70 ANGSTROM

Description

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Ligands, Modified Residues, Ions (1, 1)

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