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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE RESTRICTION-MODIFICATION CONTROLLER PROTEIN C.ESP1396I TETRAMER IN COMPLEX WITH ITS NATURAL 35 BASE-PAIR OPERATOR

Authors :   J. E. Mcgeehan, S. D. Streeter, S. J. Thresh, N. Ball, R. B. Ravelli, G. G.

Date :   18 Mar 08 (Deposition) - 29 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Protein-Dna Complex, Transcriptional Regulator, Helix-Turn-Helix, Dna-Bending, Transcription Regulator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Mcgeehan, S. D. Streeter, S. J. Thresh, N. Ball, R. B. Ravelli, G. G. Kneale
Structural Analysis Of The Genetic Switch That Regulates Th Expression Of Restriction-Modification Genes.
Nucleic Acids Res. V. 36 4778 2008
PubMed-ID: 18644840 | Reference-DOI: 10.1093/NAR/GKN448

Molecule 1 - REGULATORY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23
	Expression System Strain	:	BL21(DE3)GOLD
	Expression System Vector Type	:	PLASMID
	Gene	:	ESP1396IC
	Organism Scientific	:	ENTEROBACTER SP.
	Strain	:	RFL1396

Molecule 2 - 35-MER
	Chains	:	E
	Engineered	:	YES
	Other Details	:	OPERATOR DNA
	Other Details - Source	:	CHEMICALLY SYNTHESISED DNA
	Synthetic	:	YES

Molecule 3 - 35-MER
	Chains	:	F
	Engineered	:	YES
	Other Details	:	OPERATOR DNA
	Other Details - Source	:	CHEMICALLY SYNTHESISED DNA
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DC F:15	BINDING SITE FOR RESIDUE MG F 36

(no "SS Bond" information available for 3CLC)

(no "Cis Peptide Bond" information available for 3CLC)

(no "SAP(SNP)/Variant" information available for 3CLC)

(no "PROSITE Motif" information available for 3CLC)

(no "Exon" information available for 3CLC)

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:76
 aligned with Q8GGH0_9ENTR | Q8GGH0 from UniProtKB/TrEMBL  Length:79

    Alignment length:76
                                    11        21        31        41        51        61        71      
          Q8GGH0_9ENTR    2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
               SCOP domains d3clca_ A: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  3clc A  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
                                    11        21        31        41        51        61        71

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with Q8GGH0_9ENTR | Q8GGH0 from UniProtKB/TrEMBL  Length:79

    Alignment length:77
                                    11        21        31        41        51        61        71       
          Q8GGH0_9ENTR    2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILKH 78
               SCOP domains d3clcb_ B: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  3clc B  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILKH 78
                                    11        21        31        41        51        61        71

Chain C from PDB  Type:PROTEIN  Length:77
 aligned with Q8GGH0_9ENTR | Q8GGH0 from UniProtKB/TrEMBL  Length:79

    Alignment length:77
                                    11        21        31        41        51        61        71       
          Q8GGH0_9ENTR    2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILKH 78
               SCOP domains d3clcc_ C: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  3clc C  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILKH 78
                                    11        21        31        41        51        61        71

Chain D from PDB  Type:PROTEIN  Length:76
 aligned with Q8GGH0_9ENTR | Q8GGH0 from UniProtKB/TrEMBL  Length:79

    Alignment length:76
                                    11        21        31        41        51        61        71      
          Q8GGH0_9ENTR    2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
               SCOP domains d3clcd_ D: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  3clc D  2 ESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFEMLIKEILK 77
                                    11        21        31        41        51        61        71

Chain E from PDB  Type:DNA  Length:35
                                                                  
                  3clc E  1 ATGTGACTTATAGTCCGTGTGATTATAGTCAACAT 35
                                    10        20        30

Chain F from PDB  Type:DNA  Length:35
                                                                  
                  3clc F  1 ATGTTGACTATAATCACACGGACTATAAGTCACAT 35
                                    10        20        30

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: lambda repressor-like DNA-binding domains (180)

Superfamily: lambda repressor-like DNA-binding domains (180)

Family: automated matches (23)

Protein domain: automated matches (23)

Enterobacter sp. [TaxId: 211595] (13)

1a	d3clca_	A:
1b	d3clcb_	B:
1c	d3clcc_	C:
1d	d3clcd_	D:

(no "CATH Domain" information available for 3CLC)

(no "Pfam Domain" information available for 3CLC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q8GGH0_9ENTR | Q8GGH0)

molecular function
	GO:0003677		DNA binding		Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0043565		sequence-specific DNA binding		Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3clc)

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	3clc
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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