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(-) Description

Title :  CRYSTAL STRUCTURE OF ARAR(DBD) IN COMPLEX WITH OPERATOR ORE1
 
Authors :  D. Jain, N. Narayanan, D. T. Nair
Date :  08 Aug 15  (Deposition) - 04 Nov 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,T,U
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  T,U  (1x)
Biol. Unit 3:  A,B,T,U  (1x)
Keywords :  Arar, Transcription Factor, Winged-Helix-Turn-Helix, Dna Complex, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Jain, N. Narayanan, D. T. Nair
Plasticity In Repressor-Dna Interactions Neutralizes Loss O Symmetry In Bipartite Operators.
J. Biol. Chem. V. 291 1235 2016
PubMed-ID: 26511320  |  Reference-DOI: 10.1074/JBC.M115.689695

(-) Compounds

Molecule 1 - ARABINOSE METABOLISM TRANSCRIPTIONAL REPRESSOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDJN1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-68
    Gene: ARAR, ARAC, YVBS, BSU33970
    Organism Scientific: BACILLUS SUBTILIS (STRAIN 168)
    Organism Taxid: 224308
    Strain: 168
 
Molecule 2 - DNA (5'- D(*TP*AP*TP*AP*AP*TP*TP*AP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*AP*TP*A)- 3')
    Chains: T
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*AP*TP*AP*TP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*TP*AP*AP*TP*TP*AP*T)- 3')
    Chains: U
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABTU
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   TU
Biological Unit 3 (1x): ABTU

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5D4R)

(-) Sites  (0, 0)

(no "Site" information available for 5D4R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D4R)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Sequences/Alignments

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Chain A from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 5d4r A -13 HLEVLFQGPLGSEFMLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVSQGLLYSVQGGGTFVA  68
                                    -4         6        16        26        36        46        56        66  


Chain B from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 5d4r B  -2 SEFMLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVSQGLLYSVQGGGTFVA  68
                                     7        17        27        37        47        57        67 


Chain T from PDB  Type:DNA  Length:21
                                                     
                 5d4r T   1 TATAATTAGTACGTACAAATA  21
                                    10        20 


Chain U from PDB  Type:DNA  Length:21
                                                     
                 5d4r U  22 ATATTTGTACGTACTAATTAT  42
                                    31        41
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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 5D4R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D4R)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (5, 5)

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  5d4r
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  ARAR_BACSU | P96711
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARAR_BACSU | P96711: 3tb6 4egy 4egz 4h0e 5d4s

(-) Related Entries Specified in the PDB File

4egy 4egz 4h0e 5d4s