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Title :   CRYSTAL STRUCTURE OF THE SINGLE-STRANDED DNA-BINDING PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   K. Saikrishnan, J. Jeyakanthan, J. Venkatesh, N. Acharya, K. Sekar, U. M. Vijayan, Tb Structural Genomics Consortium (Tbsgc)

Date :   09 May 03 (Deposition) - 10 Feb 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Oligonucleotide Binding Fold, Dna-Binding Protein, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Saikrishnan, J. Jeyakanthan, J. Venkatesh, N. Acharya, K. Sekar, U. Varshney, M. Vijayan
Structure Of Mycobacterium Tuberculosis Single-Stranded Dna-Binding Protein. Variability In Quaternary Structure An Its Implications
J. Mol. Biol. V. 331 385 2003
PubMed-ID: 12888346 | Reference-DOI: 10.1016/S0022-2836(03)00729-0
(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	:	PET11D
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	SINGLE-STRANDED DNA-BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CD	2	Ligand/Ion	CADMIUM ION

Biological Unit 1 (0, 0)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:198 , ASP B:16	BINDING SITE FOR RESIDUE CD B 400
2	AC2	SOFTWARE	GLU A:100 , GLU B:62 , GLU B:65 , HOH B:402	BINDING SITE FOR RESIDUE CD B 401

(no "SS Bond" information available for 1UE5)

(no "Cis Peptide Bond" information available for 1UE5)

(no "SAP(SNP)/Variant" information available for 1UE5)

(no "PROSITE Motif" information available for 1UE5)

(no "Exon" information available for 1UE5)

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:115
 aligned with SSB_MYCTO | P9WGD4 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            SSB_MYCTO     2 AGDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d1ue5a_ A: ssDNA-binding protein                                                                                        SCOP domains
               CATH domains 1ue5A00 A:2-120 Nucleic acid-binding pro    teins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee....eeee.....eeeeeeeee......----.......eeeeeeeehhhhhhhhh......eeeeeeeeeeee.........eeeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ue5 A   2 AGDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYD----EWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31        41    |   51        61        71        81        91       101       111         
                                                                  41   46

Chain A from PDB  Type:PROTEIN  Length:115
 aligned with SSB_MYCTU | P9WGD5 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            SSB_MYCTU     2 AGDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d1ue5a_ A: ssDNA-binding protein                                                                                        SCOP domains
               CATH domains 1ue5A00 A:2-120 Nucleic acid-binding pro    teins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee....eeee.....eeeeeeeee......----.......eeeeeeeehhhhhhhhh......eeeeeeeeeeee.........eeeeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ue5 A   2 AGDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYD----EWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGPSLRYATAKVNKA 120
                                    11        21        31        41    |   51        61        71        81        91       101       111         
                                                                  41   46

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with SSB_MYCTO | P9WGD4 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
            SSB_MYCTO     3 GDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d1ue5b_ B: ssDNA-binding protein                                                                                       SCOP domains
               CATH domains 1ue5B00 B:3-120 Nucleic acid-binding prote ins                                                                         CATH domains
           Pfam domains (1) -SSB-1ue5B01 B:4-109                                                                                       ----------- Pfam domains (1)
           Pfam domains (2) -SSB-1ue5B02 B:4-109                                                                                       ----------- Pfam domains (2)
         Sec.struct. author ...eeeeeeee....eeee.....eeeeeeeee.........-.......eeeeeeeehhhhhhhhhhh....eeeeeeeeee..--------...eeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1ue5 B   3 GDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQT-EWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRS--------RTVIEVEVDEIGPSLRYATAKVNKA 120
                                    12        22        32        42 | |    52        62        72        82    |    -   |   102       112        
                                                                    44 |                                       87       96                        
                                                                      46

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with SSB_MYCTU | P9WGD5 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
            SSB_MYCTU     3 GDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGPSLRYATAKVNKA 120
               SCOP domains d1ue5b_ B: ssDNA-binding protein                                                                                       SCOP domains
               CATH domains 1ue5B00 B:3-120 Nucleic acid-binding prote ins                                                                         CATH domains
           Pfam domains (1) -SSB-1ue5B01 B:4-109                                                                                       ----------- Pfam domains (1)
           Pfam domains (2) -SSB-1ue5B02 B:4-109                                                                                       ----------- Pfam domains (2)
         Sec.struct. author ...eeeeeeee....eeee.....eeeeeeeee.........-.......eeeeeeeehhhhhhhhhhh....eeeeeeeeee..--------...eeeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1ue5 B   3 GDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQT-EWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRS--------RTVIEVEVDEIGPSLRYATAKVNKA 120
                                    12        22        32        42 | |    52        62        72        82    |    -   |   102       112        
                                                                    44 |                                       87       96                        
                                                                      46

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: ssDNA-binding protein (13)

Mycobacterium tuberculosis [TaxId: 1773] (4)

1a	d1ue5a_	A:
1b	d1ue5b_	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 tuberculosis. Organism_taxid: 1773. (4)

1a	1ue5B00	B:3-120
1b	1ue5A00	A:2-120

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: OB (224)

Family: SSB (18)

Mycobacterium tuberculosis (4)

1a	SSB-1ue5B01	B:4-109
1b	SSB-1ue5B02	B:4-109

Asymmetric Unit(hide GO term definitions)

Chain A,B (SSB_MYCTU | P9WGD5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B (SSB_MYCTO | P9WGD4)

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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UniProtKB/Swiss-Prot
	SSB_MYCTO \| P9WGD4	:	1ue1 1ue6 1ue7
	SSB_MYCTU \| P9WGD5	:	1ue1 1ue6 1ue7

1ue1	THE SAME PROTEIN WITH ZINC
1ue6	THE SAME PROTEIN WITHOUT LIGAND AT 2.7
1ue7	THE SAME PROTEIN WITHOUT LIGAND AT 3.2 RELATED ID: RV0054 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (1, 2)

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