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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COLIPHAGE LAMBDA TRANSCRIPTION ACTIVATOR PROTEIN CII
 
Authors :  A. B. Datta, S. Panjikar, M. S. Weiss, P. Chakrabarti, P. Parrack
Date :  02 Nov 04  (Deposition) - 21 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  All-Alpha Fold, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Datta, S. Panjikar, M. S. Weiss, P. Chakrabarti, P. Parrack
Structure Of {Lambda} Cii: Implications For Recognition Of Direct-Repeat Dna By An Unusual Tetrameric Organization
Proc. Natl. Acad. Sci. Usa V. 102 11242 2005
PubMed-ID: 16061804  |  Reference-DOI: 10.1073/PNAS.0504535102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN CII
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAB305
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CII
    Organism Scientific: BACTERIOPHAGE LAMBDA
    Organism Taxid: 10710

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1IPA3Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:3 , TRP B:60 , GLY B:61BINDING SITE FOR RESIDUE IPA B 101
2AC2SOFTWARELEU A:58 , HOH A:98 , LYS B:20 , VAL B:62 , VAL B:63BINDING SITE FOR RESIDUE IPA B 102
3AC3SOFTWAREARG D:69BINDING SITE FOR RESIDUE IPA D 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XWR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XWR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XWR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XWR)

(-) Exons   (0, 0)

(no "Exon" information available for 1XWR)

(-) 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:79
 aligned with RPC2_LAMBD | P03042 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:79
                                    11        21        31        41        51        61        71         
            RPC2_LAMBD    2 VRANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTN 80
               SCOP domains d1xwra1 A:2-80 Regulatory protein cII                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                  1xwr A  2 VRANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTN 80
                                    11        21        31        41        51        61        71         


Chain B from PDB  Type:PROTEIN  Length:77
 aligned with RPC2_LAMBD | P03042 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:77
                                    13        23        33        43        53        63        73       
            RPC2_LAMBD    4 ANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTN 80
               SCOP domains d1xwrb_ B: Regulatory protein cII                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  1xwr B  4 ANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTN 80
                                    13        23        33        43        53        63        73       


Chain C from PDB  Type:PROTEIN  Length:76
 aligned with RPC2_LAMBD | P03042 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:76
                                    13        23        33        43        53        63        73      
            RPC2_LAMBD    4 ANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILT 79
               SCOP domains d1xwrc_ C: Regulatory protein cII                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  1xwr C  4 ANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILT 79
                                    13        23        33        43        53        63        73      


Chain D from PDB  Type:PROTEIN  Length:77
 aligned with RPC2_LAMBD | P03042 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:77
                                    13        23        33        43        53        63        73       
            RPC2_LAMBD    4 ANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTN 80
               SCOP domains d1xwrd_ D: Regulatory protein cII                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Phage_CII-1xwrD01 D:4-80                                                      Pfam domains (1)
           Pfam domains (2) Phage_CII-1xwrD02 D:4-80                                                      Pfam domains (2)
           Pfam domains (3) Phage_CII-1xwrD03 D:4-80                                                      Pfam domains (3)
           Pfam domains (4) Phage_CII-1xwrD04 D:4-80                                                      Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  1xwr D  4 ANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTN 80
                                    13        23        33        43        53        63        73
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XWR)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RPC2_LAMBD | P03042)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  1xwr
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPC2_LAMBD | P03042: 1zpq 1zs4

(-) Related Entries Specified in the PDB File

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