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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT ORR3 IN COMPLEX WITH NTD OF ARAR
 
Authors :  D. T. Nair, D. Jain
Date :  08 Sep 12  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B,T,U
Keywords :  Winged Helix Turn Helix, Transcription Factor, Dna, 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*CP*AP*TP*TP*TP *TP*AP*T)-3'
    Chains: U
    Engineered: YES
    Other Details: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*AP*TP*AP*AP*AP*AP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*AP *AP*TP*T)-3'
    Chains: T
    Engineered: YES
    Other Details: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABTU

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:20 , ASN B:17 , HOH B:233BINDING SITE FOR RESIDUE ACT B 101
2AC2SOFTWAREGLY B:62 , DA T:5 , DA T:6 , DA T:7 , DT U:18 , DT U:19 , HOH U:216BINDING SITE FOR RESIDUE ACT U 101
3AC3SOFTWAREDG T:13 , DG T:14 , DG U:11BINDING SITE FOR RESIDUE ACT T 101
4AC4SOFTWAREGLY A:62 , HOH A:114 , DT T:20 , DT T:21 , DT U:4 , HOH U:223BINDING SITE FOR RESIDUE CA T 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H0E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H0E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H0E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H0E)

(-) Exons   (0, 0)

(no "Exon" information available for 4H0E)

(-) 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:70
                                                                                                      
               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
                 4h0e A  -1 EFMLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVSQGLLYSVQGGGTFVA  68
                                     8        18        28        38        48        58        68


Chain B from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               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
                 4h0e B -12 LEVLFQGPLGSEFMLPKYAQVKEEISSWINQGKILPDQKIPTENELMQQFGVSRHTIRKAIGDLVSQGLLYSVQGGGTFVA  68
                                    -3         7        17        27        37        47        57        67 


Chain T from PDB  Type:DNA  Length:21
                                                     
                 4h0e T   1 TATAAAATGTACGGACAAATT  21
                                    10        20 


Chain U from PDB  Type:DNA  Length:21
                                                     
                 4h0e U   1 AAATTTGTCCGTACATTTTAT  21
                                    10        20
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  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 4H0E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H0E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H0E)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  4h0e
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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 5d4r 5d4s

(-) Related Entries Specified in the PDB File

4egy ARAR-NTD-ORA COMPLEX
4egz ARAR-NTD-NATIVE ORR3 COMPLEX