3JXD - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH SYNTHETIC OPERATOR 9C IN THE PRESENCE OF RB+

Authors :   D. Watkins, G. B. Koudelka, L. D. Williams

Date :   18 Sep 09 (Deposition) - 19 Jan 10 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

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

Reference :   D. Watkins, S. Mohan, G. B. Koudelka, L. D. Williams
Sequence Recognition Of Dna By Protein-Induced Conformational Transitions.
J. Mol. Biol. V. 396 1145 2010
PubMed-ID: 20053356 | Reference-DOI: 10.1016/J.JMB.2009.12.050

*Molecule 1 - 5'- D(CPAPTPTPTPAPAPGPAPCPGPTPCPTPTPAPAPAPTP G)-3'*
	Chains	:	A, B
	Engineered	:	YES
	Other Details	:	SYNTHETIC DNA OPERATOR 9C
	Other Details - Source	:	SYNTHETIC DNA OPERATOR 9C
	Synthetic	:	YES

Molecule 2 - 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 Common	:	BACTERIOPHAGE P22
	Organism Scientific	:	ENTEROBACTERIA PHAGE P22
	Organism Taxid	:	10754

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	L	R

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	RB	2	Ligand/Ion	RUBIDIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DG A:40 , RB A:41 , DG B:20	BINDING SITE FOR RESIDUE RB A 101
2	AC2	SOFTWARE	DT A:39 , DG A:40 , RB A:101 , DG B:20	BINDING SITE FOR RESIDUE RB A 41

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_CROC1	PS50943	Cro/C1-type HTH domain profile.	RPC2_BPP22	10-64	2	L:10-64 R:10-64

(no "Exon" information available for 3JXD)

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
                                                   
                  3jxd A 21 CATTTAAGACGTCTTAAATG 40
                                    30        40

Chain B from PDB  Type:DNA  Length:20
                                                   
                  3jxd B  1 CATTTAAGACGTCTTAAATG 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 d3jxdl_ L: P22 C2 repressor, DNA-binding domain                    SCOP domains
               CATH domains 3jxdL00 L:3-68 lambda repressor-like DNA-binding domains           CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------HTH_CROC1  PDB: L:10-64 UniProt: 10-64                 ---- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3jxd 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 d3jxdr_ R: P22 C2 repressor, DNA-binding domain                    SCOP domains
               CATH domains 3jxdR00 R:3-68 lambda repressor-like DNA-binding domains           CATH domains
           Pfam domains (1) -------HTH_3-3jxdR01 R:10-64                                  ---- Pfam domains (1)
           Pfam domains (2) -------HTH_3-3jxdR02 R:10-64                                  ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------HTH_CROC1  PDB: R:10-64 UniProt: 10-64                 ---- PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3jxd 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 '\|'

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: Phage repressors (36)

Protein domain: P22 C2 repressor, DNA-binding domain (5)

Salmonella bacteriophage P22 [TaxId: 10754] (5)

1a	d3jxdl_	L:
1b	d3jxdr_	R:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: 434 Repressor (Amino-terminal Domain) (116)

Homologous Superfamily: lambda repressor-like DNA-binding domains (100)

[unclassified] (45)

1a	3jxdL00	L:3-68
1b	3jxdR00	R:3-68

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_3 (27)

Enterobacteria phage P22 (Bacteriophage P22) (3)

1a	HTH_3-3jxdR01	R:10-64
1b	HTH_3-3jxdR02	R:10-64

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.

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
		RB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3jxd
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RPC2_BPP22 \| P69202
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RPC2_BPP22 \| P69202	:	1adr 1qar 2r1j 3jxb 3jxc

3jxb	CRYSTAL STRUCTURE OF P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH SYNTHETIC OPERATOR 9C
3jxc	CRYSTAL STRUCTURE OF P22 C2 REPRESSOR PROTEIN IN COMPLEX WITH SYNTHETIC OPERATOR 9T IN THE PRESENCE OF TL+

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File