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(-) Description

Title :  CRYSTAL STRUCTURE OF SEMET NOLR FROM SINORHIZOBIUM FREDII IN COMPLEX WITH OLIGO AT DNA
 
Authors :  S. G. Lee, H. B. Krishnan, J. M. Jez
Date :  28 Jan 14  (Deposition) - 16 Apr 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.06
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Helix-Turn-Helix, Transcription Regulator, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Lee, H. B. Krishnan, J. M. Jez
Structural Basis For Regulation Of Rhizobial Nodulation And Symbiosis Gene Expression By The Regulatory Protein Nolr.
Proc. Natl. Acad. Sci. Usa V. 111 6509 2014
PubMed-ID: 24733893  |  Reference-DOI: 10.1073/PNAS.1402243111

(-) Compounds

Molecule 1 - NOLR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NOLR
    Organism Scientific: SINORHIZOBIUM FREDII
    Organism Taxid: 380
 
Molecule 2 - DNA (5 - D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)- 3 )
    Chains: E, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5 - D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)- 3 )
    Chains: F, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4OMY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OMY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OMY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OMY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OMY)

(-) Exons   (0, 0)

(no "Exon" information available for 4OMY)

(-) 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:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4omy A   6 QPLSPEKHEEAEIAAGFLSAmANPKRLLILDSLVKEEmAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVmKILGALSEIYG 102
                                    15        25|       35       |45        55        65        75        85     |  95       
                                               26-MSE           43-MSE                                          91-MSE       


Chain B from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..eehhhhhhhh..hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4omy B   6 QPLSPEKHEEAEIAAGFLSAmANPKRLLILDSLVKEEmAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVmKILGALSEIYG 102
                                    15        25|       35       |45        55        65        75        85     |  95       
                                               26-MSE           43-MSE                                          91-MSE       


Chain C from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4omy C   6 QPLSPEKHEEAEIAAGFLSAmANPKRLLILDSLVKEEmAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVmKILGALSEIYG 102
                                    15        25|       35       |45        55        65        75        85     |  95       
                                               26-MSE           43-MSE                                          91-MSE       


Chain D from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4omy D   6 QPLSPEKHEEAEIAAGFLSAmANPKRLLILDSLVKEEmAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVmKILGALSEIYG 102
                                    15        25|       35       |45        55        65        75        85     |  95       
                                               26-MSE           43-MSE                                          91-MSE       


Chain E from PDB  Type:DNA  Length:22
                                                      
                 4omy E   1 TATTAGAGAACCCTGAAGTTAA  22
                                    10        20  


Chain F from PDB  Type:DNA  Length:21
                                                     
                 4omy F   2 TTAACTTCAGGGTTCTCTAAT  22
                                    11        21 


Chain G from PDB  Type:DNA  Length:22
                                                      
                 4omy G   1 TATTAGAGAACCCTGAAGTTAA  22
                                    10        20  


Chain H from PDB  Type:DNA  Length:21
                                                     
                 4omy H   2 TTAACTTCAGGGTTCTCTAAT  22
                                    11        21
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  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 4OMY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OMY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OMY)

(-) Gene Ontology  (4, 4)

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 Related Entries

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        Q83TD2_RHIFR | Q83TD2: 4omz 4on0

(-) Related Entries Specified in the PDB File

4omz 4on0