3F6W - JenaLib

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Biological Unit 6 (Jmol Viewer)

Title :   XRE-FAMILY LIKE PROTEIN FROM PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000

Authors :   T. Petrova, M. Cuff, G. Shackleford, M. Gu, A. Joachimiak, Midwest Cen Structural Genomics (Mcsg)

Date :   06 Nov 08 (Deposition) - 02 Dec 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (2x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: B (1x),D (1x)
Biol. Unit 4: C,E  (1x)
Biol. Unit 5: C,D  (1x)
Biol. Unit 6: E  (2x)

Keywords :   Helix-Turn-Helix; Dna Binding Protein; Xenobiotic Response Element Family Of Transcriptional Regulators, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Petrova, M. Cuff, G. Shackleford, M. Gu, A. Joachimiak
Xre-Family Like Protein From Pseudomonas Syringae Pv. Tomat Str. Dc3000
To Be Published
PubMed: search

Molecule 1 - XRE-FAMILY LIKE PROTEIN
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PSPTO0717, PSPTO_0717
	Organism Scientific	:	PSEUDOMONAS SYRINGAE PV. TOMATO
	Organism Taxid	:	223283
	Strain	:	DC3000
	Synonym	:	DNA-BINDING PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	BTB	2	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	BTB	-1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 4)

No.	Name	Count	Type	Full Name
1	BTB	-1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (1, 4)

No.	Name	Count	Type	Full Name
1	BTB	-1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 6 (1, 4)

No.	Name	Count	Type	Full Name
1	BTB	-1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:-1 , SER A:-2 , ASP A:14 , GLU A:18 , HOH A:103 , HOH A:616 , ARG C:49 , ARG D:50	BINDING SITE FOR RESIDUE BTB A 81

(no "SS Bond" information available for 3F6W)

(no "Cis Peptide Bond" information available for 3F6W)

(no "SAP(SNP)/Variant" information available for 3F6W)

(no "PROSITE Motif" information available for 3F6W)

(no "Exon" information available for 3F6W)

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:82
 aligned with Q889N2_PSESM | Q889N2 from UniProtKB/TrEMBL  Length:80

    Alignment length:82
                               1                                                                                
                               |     7        17        27        37        47        57        67        77  
          Q889N2_PSESM    - ---MKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALLSKLEAMTP 79
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f6wA00 A:-2-79 lambda repressor-like DNA-binding domains                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  3f6w A -2 SNATKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFmDFCRGIGTDPYALLSKLEAmTP 79
                                     7        17        27        37        47        57        67        77  
                                                                                      57-MSE              77-MSE

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with Q889N2_PSESM | Q889N2 from UniProtKB/TrEMBL  Length:80

    Alignment length:82
                              1                                                                                
                              |      8        18        28        38        48        58        68        78  
          Q889N2_PSESM    - --MKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALLSKLEAMTPS 80
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f6wB00 B:-1-80 lambda repressor-like DNA-binding domains                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  3f6w B -1 NATKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFmDFCRGIGTDPYALLSKLEAmTPS 80
                                     8        18        28        38        48        58        68        78  
                                                                                     57-MSE              77-MSE

Chain C from PDB  Type:PROTEIN  Length:82
 aligned with Q889N2_PSESM | Q889N2 from UniProtKB/TrEMBL  Length:80

    Alignment length:82
                              1                                                                                
                              |      8        18        28        38        48        58        68        78  
          Q889N2_PSESM    - --MKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALLSKLEAMTPS 80
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f6wC00 C:-1-80 lambda repressor-like DNA-binding domains                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  3f6w C -1 NATKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFmDFCRGIGTDPYALLSKLEAmTPS 80
                                     8        18        28        38        48        58        68        78  
                                                                                     57-MSE              77-MSE

Chain D from PDB  Type:PROTEIN  Length:82
 aligned with Q889N2_PSESM | Q889N2 from UniProtKB/TrEMBL  Length:80

    Alignment length:82
                               1                                                                                
                               |     7        17        27        37        47        57        67        77  
          Q889N2_PSESM    - ---MKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALLSKLEAMTP 79
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f6wD00 D:-2-79 lambda repressor-like DNA-binding domains                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  3f6w D -2 SNATKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFmDFCRGIGTDPYALLSKLEAmTP 79
                                     7        17        27        37        47        57        67        77  
                                                                                      57-MSE              77-MSE

Chain E from PDB  Type:PROTEIN  Length:80
 aligned with Q889N2_PSESM | Q889N2 from UniProtKB/TrEMBL  Length:80

    Alignment length:80
                             1                                                                                
                             |       9        19        29        39        49        59        69        79
          Q889N2_PSESM    - -MKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALLSKLEAMTP 79
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f6wE00 E:0-79 lambda repressor-like DNA-binding domains                         CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  3f6w E  0 ATKTIHNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFmDFCRGIGTDPYALLSKLEAmTP 79
                                     9        19        29        39        49       |59        69       |79
                                                                                    57-MSE              77-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 3F6W)

Asymmetric Unit

Classes(

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

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

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

Tomato str (Pseudomonas syringae pv) (1)

1a	3f6wE00	E:0-79
1b	3f6wA00	A:-2-79
1c	3f6wB00	B:-1-80
1d	3f6wC00	C:-1-80
1e	3f6wD00	D:-2-79

(no "Pfam Domain" information available for 3F6W)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (Q889N2_PSESM | Q889N2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

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1y7y	RELATED ID: APC88786 RELATED DB: TARGETDB
2b5a
3ef8

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Ligands, Modified Residues, Ions (2, 11)

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