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

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF BACILLUS CALDOLYTICUS COLD SHOCK PROTEIN IN COMPLEX WITH HEXATHYMIDINE

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

Date :   13 Jun 06 (Deposition) - 24 Apr 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.29

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

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

Reference :   K. E. Max, M. Zeeb, R. Bienert, J. Balbach, U. Heinemann
Common Mode Of Dna Binding To Cold Shock Domains. Crystal Structure Of Hexathymidine Bound To The Domain-Swapped Form Of A Major Cold Shock Protein From Bacillus Caldolyticus.
Febs J. V. 274 1265 2007
PubMed-ID: 17266726 | Reference-DOI: 10.1111/J.1742-4658.2007.05672.X
(for further references see the PDB file header)

*Molecule 1 - 5'-D(TPTPTPTPTPT)-3'*
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SYNTHETIC DEOXYRIBONUCLEOTIDE
	Synonym	:	HEXATHYMIDINE
	Synthetic	:	YES

Molecule 2 - COLD SHOCK PROTEIN CSPB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CSPB
	Organism Scientific	:	BACILLUS CALDOLYTICUS
	Organism Taxid	:	1394

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DT C:6 , HOH C:113 , HOH C:114 , HOH D:10 , HOH D:11 , HOH D:12 , HOH D:36	BINDING SITE FOR RESIDUE CA C 235
2	AC2	SOFTWARE	GLY A:54 , ASN A:55 , HOH A:386 , VAL B:52 , DT D:3	BINDING SITE FOR RESIDUE MPD A 301
3	AC3	SOFTWARE	VAL A:52 , HOH A:304 , ASN B:55 , HOH B:451 , DT C:3 , HOH C:161	BINDING SITE FOR RESIDUE MPD B 401

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

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

(no "SAP(SNP)/Variant" information available for 2HAX)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COLD_SHOCK	PS00352	'Cold-shock' domain signature.	CSPB_BACCL	15-33	2	A:15-33 B:15-33

(no "Exon" information available for 2HAX)

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
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Chain A from PDB  Type:PROTEIN  Length:66
 aligned with CSPB_BACCL | P41016 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
            CSPB_BACCL    1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
               SCOP domains d2haxa_ A: Major cold shock protein                                SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeee..eeeeeee.hhh............eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------COLD_SHOCK         --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2hax A  1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:66
 aligned with CSPB_BACCL | P41016 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
            CSPB_BACCL    1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
               SCOP domains d2haxb_ B: Major cold shock protein                                SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee....eeeee......eeee.hhh............eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------COLD_SHOCK         --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2hax B  1 MQRGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAANVVKL 66
                                    10        20        30        40        50        60

Chain C from PDB  Type:DNA  Length:6
                                     
                  2hax C  1 TTTTTT  6

Chain D from PDB  Type:DNA  Length:6
                                     
                  2hax D  1 TTTTTT  6

Legend:		→ Mismatch	(orange background)
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	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/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 caldolyticus [TaxId: 1394] (7)

1a	d2haxa_	A:
1b	d2haxb_	B:

(no "CATH Domain" information available for 2HAX)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CSPB_BACCL | P41016)

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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 2hax)

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	CSPB_BACCL \| P41016	:	1c9o 1hz9 1hza 1hzb 1hzc 1i5f 5jx4

1c9o	BACILLUS CALDOLYTICUS COLD SHOCK PROTEIN
1csp	BACILLUS SUBTILIS COLD SHOCK PROTEIN B
1mjc	ESCHERICHIA COLI COLD SHOCK PROTEIN A
2es2	BACILLUS SUBTILIS COLD SHOCK PROTEIN B IN COMPLEX WITH HEXATHYMIDINE

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