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(-) Description

Title :  ANTITOXIN PHD FROM PHAGE P1 IN COMPLEX WITH ITS OPERATOR DNA INVERTED REPEAT
 
Authors :  A. Garcia-Pino, R. Loris
Date :  02 May 15  (Deposition) - 20 Apr 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.17
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,G,H  (1x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Transcription Factor, Toxin-Antitoxin, Dna Binding, Intrinsic Disorder, Conditional Cooperativity, Protein-Dna Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Garcia-Pino, S. De Gieter, A. Talavera, H. De Greve, R. G. Efremov R. Loris
An Intrinsically Disordered Entropic Switch Determines Allostery In Phd-Doc Regulation.
Nat. Chem. Biol. V. 12 490 2016
PubMed-ID: 27159580  |  Reference-DOI: 10.1038/NCHEMBIO.2078

(-) Compounds

Molecule 1 - ANTITOXIN PHD
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    GenePHD
    Organism ScientificENTEROBACTERIA PHAGE P1
    Organism Taxid10678
    Other DetailsTHE C-TERMINAL REGION OF THE PROTEIN IS INTRINSICALLY DISORDERED
    SynonymADDICTION PROTEIN PDH,PREVENT HOST DEATH PROTEIN
 
Molecule 2 - DNA/RNA (5'-D(CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')
    ChainsE, G
    EngineeredYES
    Organism ScientificENTEROBACTERIA PHAGE P1
    Organism Taxid10678
    SyntheticYES
 
Molecule 3 - DNA/RNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*A)-3')
    ChainsF, H
    EngineeredYES
    Organism ScientificENTEROBACTERIA PHAGE P1
    Organism Taxid10678
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB    GH
Biological Unit 2 (1x)  CDEF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
11442Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11442Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1144-1Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:12 , GLU A:15 , DG G:7 , DT G:8binding site for residue 144 G 101
2AC2SOFTWAREDT G:6 , DA H:13 , DG H:14binding site for residue 144 G 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZM0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg D:31 -Gly D:32
2Gly D:32 -Arg D:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZM0)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZM0)

(-) 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:55
                                                                                      
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeeee..eeeeeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  4zm0 A  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAE 55
                                    10        20        30        40        50     

Chain B from PDB  Type:PROTEIN  Length:57
                                                                                        
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  4zm0 B  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFA 57
                                    10        20        30        40        50       

Chain C from PDB  Type:PROTEIN  Length:55
                                                                                      
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeeee..eeeeeeeehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  4zm0 C  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAE 55
                                    10        20        30        40        50     

Chain D from PDB  Type:PROTEIN  Length:54
                                                                                     
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  4zm0 D  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDA 54
                                    10        20        30        40        50    

Chain E from PDB  Type:DNA  Length:13
                                            
                  4zm0 E  2 CTTGTGTACACAT 14
                                    11   

Chain F from PDB  Type:DNA  Length:13
                                            
                  4zm0 F  1 CATGTGTACACAA 13
                                    10   

Chain G from PDB  Type:DNA  Length:14
                                             
                  4zm0 G  1 GCTTGTGTACACAT 14
                                    10    

Chain H from PDB  Type:DNA  Length:14
                                             
                  4zm0 H  1 CATGTGTACACAAG 14
                                    10    

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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 4ZM0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZM0)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHD_BPP1 | Q062533dd7 3hry 3hs2 3k33 3kh2 4zlx 4zm2

(-) Related Entries Specified in the PDB File

4zlx 4ZLX CONTAINS THE UNBOUND DNA BINDING DOMAIN OF PHD