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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE TRPR PROTEIN FROM RUMINOCOCCUS OBEUM
 
Authors :  J. Osipiuk, L. Keigher, R. Jedrzejczak, G. Babnigg, A. Joachimiak, Mid Center For Structural Genomics (Mcsg)
Date :  08 Jan 09  (Deposition) - 20 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,D  (1x)
Biol. Unit 2:  C,D,F  (1x)
Biol. Unit 3:  B,E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Structural Genomics, Apc21159, Trpr, Trp Repressor, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, L. Keigher, R. Jedrzejczak, G. Babnigg, A. Joachimiak
X-Ray Crystal Structure Of Putative Trpr Protein From Ruminococcus Obeum.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE TRP REPRESSOR PROTEIN
    Atcc: 29174
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RUMOBE_00155
    Organism Scientific: RUMINOCOCCUS OBEUM ATCC 29174
    Organism Taxid: 411459

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB D    
Biological Unit 2 (1x):   CD F  
Biological Unit 3 (1x):  B  EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric Unit (2, 27)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 6)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:37 , LEU B:40 , SER B:41 , GLN B:44 , LYS F:3BINDING SITE FOR RESIDUE ACT B 202
2AC2SOFTWAREASP C:32 , VAL C:33 , HOH C:414 , ARG D:45 , SER D:78 , HOH D:340BINDING SITE FOR RESIDUE ACT D 203
3AC3SOFTWARELYS E:23 , ARG F:6 , ASP F:11BINDING SITE FOR RESIDUE ACT F 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FRW)

(-) 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:94
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:94
                                    14        24        34        44        54        64        74        84        94    
          A5ZMD8_9FIRM    5 IRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEKET 98
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3frw A  5 IRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEKET 98
                                    14        24        34        44      | 54        64        74        84   |    94    
                                                                         51-MSE                               88-MSE|     
                                                                                                                   93-MSE 


Chain B from PDB  Type:PROTEIN  Length:96
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
          A5ZMD8_9FIRM    2 GKKIRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEKE 97
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  3frw B  2 GKKIRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEKE 97
                                    11        21        31        41        51        61        71        81      | 91 |    
                                                                            51-MSE                               88-MSE|    
                                                                                                                      93-MSE


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:93
                                    15        25        35        45        55        65        75        85        95   
          A5ZMD8_9FIRM    6 RTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEKET 98
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3frw C  6 RTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEKET 98
                                    15        25        35        45     |  55        65        75        85  |    |95   
                                                                        51-MSE                               88-MSE|     
                                                                                                                  93-MSE 


Chain D from PDB  Type:PROTEIN  Length:92
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:92
                                    14        24        34        44        54        64        74        84        94  
          A5ZMD8_9FIRM    5 IRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEK 96
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3frw D  5 IRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEK 96
                                    14        24        34        44      | 54        64        74        84   |    94  
                                                                         51-MSE                               88-MSE|   
                                                                                                                   93-MSE


Chain E from PDB  Type:PROTEIN  Length:96
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:96
                                    13        23        33        43        53        63        73        83        93      
          A5ZMD8_9FIRM    4 KIRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEKETA 99
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  3frw E  4 KIRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEKETA 99
                                    13        23        33        43       |53        63        73        83    |   93      
                                                                          51-MSE                               88-MSE|      
                                                                                                                    93-MSE  


Chain F from PDB  Type:PROTEIN  Length:94
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:94
                                    12        22        32        42        52        62        72        82        92    
          A5ZMD8_9FIRM    3 KKIRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEK 96
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3frw F  3 KKIRTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEK 96
                                    12        22        32        42        52        62        72        82     |  92|   
                                                                           51-MSE                               88-MSE|   
                                                                                                                     93-MSE


Chain G from PDB  Type:PROTEIN  Length:92
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:92
                                    15        25        35        45        55        65        75        85        95  
          A5ZMD8_9FIRM    6 RTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEKE 97
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3frw G  6 RTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEKE 97
                                    15        25        35        45     |  55        65        75        85  |    |95  
                                                                        51-MSE                               88-MSE|    
                                                                                                                  93-MSE


Chain H from PDB  Type:PROTEIN  Length:93
 aligned with A5ZMD8_9FIRM | A5ZMD8 from UniProtKB/TrEMBL  Length:104

    Alignment length:93
                                    15        25        35        45        55        65        75        85        95   
          A5ZMD8_9FIRM    6 RTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEMVFSRMKEKET 98
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3frw H  6 RTEEVDHLFEAILCLKNKEECYTFFEDVCTINELLSLSQRFEVAKmLTDKRTYLDISEKTGASTATISRVNRSLNYGNDGYEmVFSRmKEKET 98
                                    15        25        35        45     |  55        65        75        85  |    |95   
                                                                        51-MSE                               88-MSE|     
                                                                                                                  93-MSE
   Legend:   → Mismatch (orange background)
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    → 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 3FRW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (A5ZMD8_9FIRM | A5ZMD8)
molecular function
    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.
    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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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