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(-) Description

Title :  CRYSTAL STRUCTURE OF ARAR(DBD) IN COMPLEX WITH OPERATOR ORR3
 
Authors :  D. Jain, D. T. Nair
Date :  02 Apr 12  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,T,U
Keywords :  Winged-Helix-Turn-Helix, Transcription Factor, Dna Binding, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Jain, D. T. Nair
Spacing Between Core Recognition Motifs Determines Relative Orientation Of Arar Monomers On Bipartite Operators.
Nucleic Acids Res. V. 41 639 2013
PubMed-ID: 23109551  |  Reference-DOI: 10.1093/NAR/GKS962

(-) Compounds

Molecule 1 - ARABINOSE METABOLISM TRANSCRIPTIONAL REPRESSOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDJN1
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINUS DOMAIN, UNP RESIDUES 1-68
    Gene: ARAC, ARAR, BSU33970, YVBS
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
 
Molecule 2 - 5'-D(*AP*AP*AP*TP*TP*TP*GP*TP*CP*CP*GP*TP*AP*TP*AP*CP*AP*TP *TP*TP*T)-3'
    Chains: T
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*AP*AP*AP*AP*TP*GP*TP*AP*TP*AP*CP*GP*GP*AP*CP*AP*AP *AP*TP*T)-3'
    Chains: U
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABTU

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:213BINDING SITE FOR RESIDUE ACT A 101
2AC2SOFTWARETYR A:5 , LYS A:46 , ASP A:50 , DT U:708BINDING SITE FOR RESIDUE ACT A 102
3AC3SOFTWAREGLN A:18 , LYS A:20 , LYS B:4BINDING SITE FOR RESIDUE ACT B 101
4AC4SOFTWAREDA T:701 , DT T:702 , DT U:699 , DT U:718 , DT U:719 , HOH U:819BINDING SITE FOR RESIDUE ACT T 801
5AC5SOFTWAREARG B:41 , DT T:712 , DA T:713 , HOH T:911BINDING SITE FOR RESIDUE ACT T 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EGZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee..hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 4egz A -12 LEVLFQGPLGSEFMLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVSQGLLYSVQGGGTFVA  68
                                    -3         7        17        27        37        47        57        67 


Chain B from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               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
                 4egz B -14 HHLEVLFQGPLGSEFMLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVSQGLLYSVQGGGTFVA  68
                                    -5         5        15        25        35        45        55        65   


Chain T from PDB  Type:DNA  Length:21
                                                     
                 4egz T 699 AAATTTGTCCGTATACATTTT 719
                                   708       718 


Chain U from PDB  Type:DNA  Length:21
                                                     
                 4egz U 699 TAAAATGTATACGGACAAATT 719
                                   708       718
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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 4EGZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  4egz
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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 4h0e 5d4r 5d4s

(-) Related Entries Specified in the PDB File

4egy