3PQJ - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

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

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

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

Method :   X-RAY DIFFRACTION

Resolution :   2.48

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (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
	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
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3PQJ)

(no "Site" information available for 3PQJ)

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

Asymmetric Unit

No.	Residues
1	Gln A:62	-	Pro A:63
2	Gln C:62	-	Pro C:63

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

Asymmetric Unit (1, 4)

	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	4	A:17-110 B:17-109 C:17-110 D:17-108

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:17-110 B:17-109 - -

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:17-110 D:17-108

(no "Exon" information available for 3PQJ)

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:98
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:98
                                    22        32        42        52        62        72        82        92       102        
           BIGR_XYLFA    13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQ 110
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh...hhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HTH_ARSR_2  PDB: A:17-110 UniProt: 17-111                                                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3pqj A  13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQ 110
                                    22        32        42        52        62        72        82        92       102

Chain B from PDB  Type:PROTEIN  Length:91
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:97
                                    22        32        42        52        62        72        82        92       102       
           BIGR_XYLFA    13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCA 109
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh.------hhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HTH_ARSR_2  PDB: B:17-109 UniProt: 17-111                                                     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3pqj B  13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGI------QQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCA 109
                                    22        32        42        52       | -    |   72        82        92       102       
                                                                          60     67

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:98
                                    22        32        42        52        62        72        82        92       102        
           BIGR_XYLFA    13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQ 110
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh...hhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HTH_ARSR_2  PDB: C:17-110 UniProt: 17-111                                                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3pqj C  13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFCAQ 110
                                    22        32        42        52        62        72        82        92       102

Chain D from PDB  Type:PROTEIN  Length:90
 aligned with BIGR_XYLFA | Q9PFB1 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:96
                                    22        32        42        52        62        72        82        92       102      
           BIGR_XYLFA    13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFC 108
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------HTH_20-3pqjD01 D:26-84                                     ------------------------ Pfam domains (1)
           Pfam domains (2) -------------HTH_20-3pqjD02 D:26-84                                     ------------------------ Pfam domains (2)
           Pfam domains (3) -------------HTH_20-3pqjD03 D:26-84                                     ------------------------ Pfam domains (3)
           Pfam domains (4) -------------HTH_20-3pqjD04 D:26-84                                     ------------------------ Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...eehhhhhhhhh.------hhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----HTH_ARSR_2  PDB: D:17-108 UniProt: 17-111                                                    PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3pqj D  13 MTREDMEKRANEVANLLKTLSHPVRLMLVCTLVEGEFSVGELEQQIGI------QQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTIFC 108
                                    22        32        42        52       | -    |   72        82        92       102      
                                                                          60     67

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 3PQJ)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: HTH_20 (11)

Xylella fastidiosa (2)

1a	HTH_20-3pqjD01	D:26-84
1b	HTH_20-3pqjD02	D:26-84
1c	HTH_20-3pqjD03	D:26-84
1d	HTH_20-3pqjD04	D:26-84

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3pqj)

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

	Cis Peptide Bonds
		Gln A:62 - Pro A:63	[ RasMol ]
		Gln C:62 - Pro C:63	[ RasMol ]

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

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	3pqj
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	BIGR_XYLFA \| Q9PFB1
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	BIGR_XYLFA \| Q9PFB1	:	3pqk

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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