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(-) Description

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

(-) Compounds

Molecule 1 - XRE-FAMILY LIKE PROTEIN
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePSPTO0717, PSPTO_0717
    Organism ScientificPSEUDOMONAS SYRINGAE PV. TOMATO
    Organism Taxid223283
    StrainDC3000
    SynonymDNA-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (2x)A    
Biological Unit 2 (1x)AB   
Biological Unit 3 (1x) B (1x) D (1x) 
Biological Unit 4 (1x)  C E
Biological Unit 5 (1x)  CD 
Biological Unit 6 (2x)    E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1BTB2Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1BTB-1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1BTB-1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1BTB-1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 6 (1, 4)
No.NameCountTypeFull Name
1BTB-1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:-1 , SER A:-2 , ASP A:14 , GLU A:18 , HOH A:103 , HOH A:616 , ARG C:49 , ARG D:50BINDING SITE FOR RESIDUE BTB A 81

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3F6W)

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (1, 5)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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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(-) Related Entries Specified in the PDB File

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