2R1J - JenaLib

Title :   CRYSTAL STRUCTURE OF THE P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH THE SYNTHETIC OPERATOR 9T

Authors :   L. D. Williams, G. B. Koudelka, D. Watkins, C. Hsiao, K. Woods

Date :   22 Aug 07 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.53

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

Keywords :   Protein-Dna Complex, Helix-Turn-Helix, Dna-Binding, Repressor, Transcription, Transcription Regulation, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Watkins, C. Hsiao, K. K. Woods, G. B. Koudelka, L. D. Williams
P22 C2 Repressor-Operator Complex: Mechanisms Of Direct And Indirect Readout
Biochemistry V. 47 2325 2008
PubMed-ID: 18237194 | Reference-DOI: 10.1021/BI701826F
(for further references see the PDB file header)

Compounds

*Molecule 1 - 5'- D(DCPDAPDTPDTPDTPDAPDAPDGPDAPDTPDAPDTPDCPDTP DTPDAPDAPDAPDTPDA)-3'*
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(DTPDAPDTPDTPDTPDAPDAPDGPDAPDTPDAPDTPDCPDTP DTPDAPDAPDAPDTPDG)-3'*
	Chains	:	A
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - REPRESSOR PROTEIN C2
	Chains	:	L, R
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC18
	Expression System Strain	:	XA90
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	C2
	Organism Scientific	:	ENTEROBACTERIA PHAGE P22
	Organism Taxid	:	10754

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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:DNA  Length:20
                                                   
                  2r1j A 21 TATTTAAGATATCTTAAATG 40
                                    30        40

Chain B from PDB  Type:DNA  Length:20
                                                   
                  2r1j B  1 CATTTAAGATATCTTAAATA 20
                                    10        20

Chain L from PDB  Type:PROTEIN  Length:66
 aligned with RPC2_BPP22 | P69202 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                    12        22        32        42        52        62      
            RPC2_BPP22    3 TQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
               SCOP domains d2r1jl_ L: P22 C2 repressor, DNA-binding domain                    SCOP domains
               CATH domains 2r1jL00 L:3-68 lambda repressor-like DNA-binding domains           CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------HTH_CROC1  PDB: L:10-64 UniProt: 10-64                 ---- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2r1j L  3 TQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
                                    12        22        32        42        52        62

Chain R from PDB  Type:PROTEIN  Length:66
 aligned with RPC2_BPP22 | P69202 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:66
                                    12        22        32        42        52        62      
            RPC2_BPP22    3 TQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
               SCOP domains d2r1jr_ R: P22 C2 repressor, DNA-binding domain                    SCOP domains
               CATH domains 2r1jR00 R:3-68 lambda repressor-like DNA-binding domains           CATH domains
           Pfam domains (1) -------HTH_3-2r1jR01 R:10-64                                  ---- Pfam domains (1)
           Pfam domains (2) -------HTH_3-2r1jR02 R:10-64                                  ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------HTH_CROC1  PDB: R:10-64 UniProt: 10-64                 ---- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2r1j R  3 TQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD 68
                                    12        22        32        42        52        62

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, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain L,R (RPC2_BPP22 | P69202)

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.
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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2r1j)

	Sites
(no "Sites" information available for 2r1j)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2r1j)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2r1j
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RPC2_BPP22 \| P69202
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description