3PQK - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TRANSCRIPTIONAL REPRESSOR BIGR FROM XYLELLA FASTIDIOSA

Authors :   C. E. Benedetti, B. G. Guimaraes

Date :   26 Nov 10 (Deposition) - 01 Jun 11 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Helix-Turn-Helix Motif, Winged-Helix Fold, Transcriptional Repressor, Dna Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. G. Guimaraes, R. L. Barbosa, A. S. Soprano, B. M. Campos, T. A. De Souza, C. C. Tonoli, A. F. Leme, M. T. Murakami, C. E. Benedetti
Plant Pathogenic Bacteria Utilize Biofilm Growth-Associated Repressor (Bigr), A Novel Winged-Helix Redox Switch, To Control Hydrogen Sulfide Detoxification Under Hypoxia.
J. Biol. Chem. V. 286 26148 2011
PubMed-ID: 21632538 | Reference-DOI: 10.1074/JBC.M111.234039

Molecule 1 - BIOFILM GROWTH-ASSOCIATED REPRESSOR
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 13-114
	Gene	:	BIGR, XF_0767
	Organism Scientific	:	XYLELLA FASTIDIOSA
	Organism Taxid	:	2371

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3PQK)

Asymmetric Unit

No.	Residues
1	A:42	-	A:108
2	B:42	-	B:108
3	C:42	-	C:108
4	D:42	-	D:108
5	E:42	-	E:108
6	F:42	-	F:108

Asymmetric Unit

No.	Residues
1	Gln A:62	-	Pro A:63
2	Gln B:62	-	Pro B:63
3	Gln C:62	-	Pro C:63
4	Gln D:62	-	Pro D:63
5	Gln E:62	-	Pro E:63
6	Gln F:62	-	Pro F:63

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	BIGR_XYLFA	17-111	6	A:17-111 B:17-111 C:17-111 D:17-111 E:17-111 F:17-111

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	BIGR_XYLFA	17-111	2	A:17-111 B:17-111 - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	BIGR_XYLFA	17-111	2	- - C:17-111 D:17-111 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_ARSR_2	PS50987	ArsR-type HTH domain profile.	BIGR_XYLFA	17-111	2	- - - - E:17-111 F:17-111

(no "Exon" information available for 3PQK)

Asymmetric 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:99
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:99
                                    25        35        45        55        65        75        85        95       105         
           BIGR_XYLFA    16 EDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..eeee......eeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_ARSR_2  PDB: A:17-111 UniProt: 17-111                                                      --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3pqk A  16 EDMEKRANEVANLLKTLSHPVRLmLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
                                    25        35   |    45        55        65        75        85        95       105         
                                                  39-MSE

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:101
                                    23        33        43        53        63        73        83        93       103       113 
           BIGR_XYLFA    14 TREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..eeee......eeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_ARSR_2  PDB: B:17-111 UniProt: 17-111                                                      --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3pqk B  14 TREDMEKRANEVANLLKTLSHPVRLmLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
                                    23        33     |  43        53        63        73        83        93       103       113 
                                                    39-MSE

Chain C from PDB  Type:PROTEIN  Length:101
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:101
                                    23        33        43        53        63        73        83        93       103       113 
           BIGR_XYLFA    14 TREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..eeee......eeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_ARSR_2  PDB: C:17-111 UniProt: 17-111                                                      --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3pqk C  14 TREDMEKRANEVANLLKTLSHPVRLmLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
                                    23        33     |  43        53        63        73        83        93       103       113 
                                                    39-MSE

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:101
                                    23        33        43        53        63        73        83        93       103       113 
           BIGR_XYLFA    14 TREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..eeee......eeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_ARSR_2  PDB: D:17-111 UniProt: 17-111                                                      --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3pqk D  14 TREDMEKRANEVANLLKTLSHPVRLmLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
                                    23        33     |  43        53        63        73        83        93       103       113 
                                                    39-MSE

Chain E from PDB  Type:PROTEIN  Length:101
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:101
                                    23        33        43        53        63        73        83        93       103       113 
           BIGR_XYLFA    14 TREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..eeee......eeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_ARSR_2  PDB: E:17-111 UniProt: 17-111                                                      --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3pqk E  14 TREDMEKRANEVANLLKTLSHPVRLmLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
                                    23        33     |  43        53        63        73        83        93       103       113 
                                                    39-MSE

Chain F from PDB  Type:PROTEIN  Length:100
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:100
                                    24        34        44        54        64        74        84        94       104       114
           BIGR_XYLFA    15 REDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------HTH_20-3pqkF01 F:26-84                                     ------------------------------ Pfam domains (1)
           Pfam domains (2) -----------HTH_20-3pqkF02 F:26-84                                     ------------------------------ Pfam domains (2)
           Pfam domains (3) -----------HTH_20-3pqkF03 F:26-84                                     ------------------------------ Pfam domains (3)
           Pfam domains (4) -----------HTH_20-3pqkF04 F:26-84                                     ------------------------------ Pfam domains (4)
           Pfam domains (5) -----------HTH_20-3pqkF05 F:26-84                                     ------------------------------ Pfam domains (5)
           Pfam domains (6) -----------HTH_20-3pqkF06 F:26-84                                     ------------------------------ Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..eeee......eeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --HTH_ARSR_2  PDB: F:17-111 UniProt: 17-111                                                      --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3pqk F  15 REDMEKRANEVANLLKTLSHPVRLmLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQEKQA 114
                                    24        34    |   44        54        64        74        84        94       104       114
                                                   39-MSE

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 '\|'

(no "SCOP Domain" information available for 3PQK)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_20 (11)

Xylella fastidiosa (2)

1a	HTH_20-3pqkF01	F:26-84
1b	HTH_20-3pqkF02	F:26-84
1c	HTH_20-3pqkF03	F:26-84
1d	HTH_20-3pqkF04	F:26-84
1e	HTH_20-3pqkF05	F:26-84
1f	HTH_20-3pqkF06	F:26-84

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (BIGR_XYLFA | Q9PFB1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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 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
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3pqk)

	Cis Peptide Bonds
		Gln A:62 - Pro A:63	[ RasMol ]
		Gln B:62 - Pro B:63	[ RasMol ]
		Gln C:62 - Pro C:63	[ RasMol ]
		Gln D:62 - Pro D:63	[ RasMol ]
		Gln E:62 - Pro E:63	[ RasMol ]
		Gln F:62 - Pro F:63	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 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
	3pqk
		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
	BIGR_XYLFA \| Q9PFB1
		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
	BIGR_XYLFA \| Q9PFB1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BIGR_XYLFA \| Q9PFB1	:	3pqj

3pqj	REDUCED FORM OF BIGR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 6)

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