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Asym./Biol. Unit

Asym./Biol. Unit - sites

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE BACILLUS SUBTILIS COLD SHOCK PROTEIN BS-CSPB IN COMPLEX WITH HEXATHYMIDINE

Authors :   K. E. A. Max, M. Bienert, U. Heinemann

Date :   25 Oct 05 (Deposition) - 05 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

Chains :   Asym./Biol. Unit : A,B

Keywords :   Beta Barrel, Protein-Dna Complex, Single-Stranded Dna, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. E. Max, M. Zeeb, R. Bienert, J. Balbach, U. Heinemann
T-Rich Dna Single Strands Bind To A Preformed Site On The Bacterial Cold Shock Protein Bs-Cspb.
J. Mol. Biol. V. 360 702 2006
PubMed-ID: 16780871 | Reference-DOI: 10.1016/J.JMB.2006.05.044

Compounds

*Molecule 1 - 5'-D(TPTPTPTPTPT)-3'*
	Chains	:	B
	Engineered	:	YES
	Other Details	:	DNA SYNTHESIS
	Synonym	:	HEXATHYMIDINE
	Synthetic	:	YES

Molecule 2 - COLD SHOCK PROTEIN CSPB
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	CSPB, CSPA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	MAJOR COLD SHOCK PROTEIN

Structural Features

Chains, Units

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:1 , GLU A:3 , ASP A:24 , HOH A:211 , HOH A:228 , HOH A:250	BINDING SITE FOR RESIDUE CA A 100
2	AC2	SOFTWARE	PHE A:9 , GLU A:43 , HOH A:213	BINDING SITE FOR RESIDUE CA A 200

SS Bonds (0, 0)

(no "SS Bond" information available for 2ES2)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2ES2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CSPB_BACSU_001 *	F	17	L	CSPB_BACSU	---	---	A	F	17	L
2	UniProt	VAR_CSPB_BACSU_002 *	G	44	S	CSPB_BACSU	---	---	A	G	44	S
3	UniProt	VAR_CSPB_BACSU_003 *	A	46	S	CSPB_BACSU	---	---	A	A	46	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COLD_SHOCK	PS00352	'Cold-shock' domain signature.	CSPB_BACSU	15-33	1	A:15-33

Exons (0, 0)

(no "Exon" information available for 2ES2)

Sequences/Alignments

Asymmetric/Biological 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:67
 aligned with CSPB_BACSU | P32081 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:67
                                    10        20        30        40        50        60       
            CSPB_BACSU    1 MLEGKVKWFNSEKGFGFIEVEGQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAANVTKEA 67
               SCOP domains d2es2a_ A: Major cold shock protein                                 SCOP domains
               CATH domains 2es2A00 A:1-67 Nucleic acid-binding proteins                        CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....eeeee......eeee.hhh............eeeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------L--------------------------S-S--------------------- SAPs(SNPs)
                    PROSITE --------------COLD_SHOCK         ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2es2 A  1 MLEGKVKWFNSEKGFGFIEVEGQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAANVTKEA 67
                                    10        20        30        40        50        60

Chain B from PDB  Type:DNA  Length:6
                                     
                  2es2 B  1 TTTTTT  6

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: Cold shock DNA-binding domain-like (310)

Protein domain: Major cold shock protein (21)

Bacillus subtilis [TaxId: 1423] (10)

d2es2a_

CATH Domains (1, 1)

Asymmetric/Biological 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)

[unclassified] (49)

2es2A00

A:1-67

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2ES2)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CSPB_BACSU | P32081)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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Asymmetric/Biological Unit
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Still Images

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	2es2
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CSPB_BACSU \| P32081	:	1csp 1csq 1nmf 1nmg 2f52 2i5l 2i5m 3pf4 3pf5

Related Entries Specified in the PDB File

1csp	UNIVERSAL NUCLEIC ACID-BINDING DOMAIN REVEALED BY CRYSTAL STRUCTURE OF THE B. SUBTILIS MAJOR COLD-SHOCK PROTEIN.
1csq	UNIVERSAL NUCLEIC ACID-BINDING DOMAIN REVEALED BY CRYSTAL STRUCTURE OF THE B. SUBTILIS MAJOR COLD-SHOCK PROTEIN.