1X3E - JenaLib

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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 K. Muniyappa, M. Vijayan

Date :   04 May 05 (Deposition) - 15 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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	GLU A:100 , HOH A:1086 , GLU B:62 , GLU B:65	BINDING SITE FOR RESIDUE CD A 1001

(no "SS Bond" information available for 1X3E)

(no "Cis Peptide Bond" information available for 1X3E)

(no "SAP(SNP)/Variant" information available for 1X3E)

(no "PROSITE Motif" information available for 1X3E)

(no "Exon" information available for 1X3E)

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:110
 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 d1x3ea_ A: automated matches                                                                                           SCOP domains
               CATH domains 1x3eA00 A:3-120 Nucleic acid-binding       proteins                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eeee.....eeeeeeee.....------........eeeeeeehhhhhhhhhhh....eeeeeeeeeeeeee..--.eeeeeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1x3e A   3 GDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRM------EWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETR--EKRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    12        22        32      |  -   |    52        62        72        82        |- |     102       112        
                                                               39     46                                           91 94

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with SSB_MYCS2 | Q9AFI5 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            SSB_MYCS2     2 AGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d1x3eb_ B: automated matches                                                                                            SCOP domains
               CATH domains 1x3eB00 B:2-120 Nucleic acid-binding proteins                                                                           CATH domains
           Pfam domains (1) --SSB-1x3eB01 B:4-109                                                                                       ----------- Pfam domains (1)
           Pfam domains (2) --SSB-1x3eB02 B:4-109                                                                                       ----------- Pfam domains (2)
         Sec.struct. author ....eeeeeeee....eeee.....eeeeeeeee..ee........ee...eeeeeeeehhhhhhhhhhh....eeeeeeeeeeee.........eeeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1x3e B   2 AGDTTITVVGNLTADPELRFTPSGAAVANFTVASTPRMFDRQSGEWKDGEALFLRCNIWREAAENVAESLTRGSRVIVTGRLKQRSFETREGEKRTVVEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31        41        51        61        71        81        91       101       111

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	d1x3ea_	A:
1b	d1x3eb_	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	1x3eA00	A:3-120
1b	1x3eB00	B:2-120

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: OB (224)

Family: SSB (18)

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

1a	SSB-1x3eB01	B:4-109
1b	SSB-1x3eB02	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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	1x3e
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	SSB_MYCS2 \| Q9AFI5	:	1x3f 1x3g 3a5u

1x3f	THE SAME PROTEIN AT 2.70 ANGSTROM
1x3g	THE SAME PROTEIN AT 3.00 ANGSTROM

Description

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Ligands, Modified Residues, Ions (1, 1)

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