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(-) Description

Title :  UNBOUND OXIDISED CPRK
 
Authors :  C. Levy
Date :  14 Aug 08  (Deposition) - 30 Sep 08  (Release) - 23 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Cprk, Halorespiration, Transcriptional Regulator, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Levy, K. Pike, D. J. Heyes, M. G. Joyce, K. Gabor, H. Smidt, J. Van Der Oost, D. Leys
Molecular Basis Of Halorespiration Control By Cprk, A Crp-Fnr Type Transcriptional Regulator
Mol. Microbiol. V. 70 151 2008
PubMed-ID: 18717788  |  Reference-DOI: 10.1111/J.1365-2958.2008.06399.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLIC NUCLEOTIDE-BINDING PROTEIN
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRC99
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDHAF_0678
    Organism ScientificDESULFITOBACTERIUM HAFNIENSE
    Organism Taxid272564
    StrainDCB-2
    SynonymCPRK

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3E5Q)

(-) Sites  (0, 0)

(no "Site" information available for 3E5Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E5Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln F:140 -Val F:141
2Val F:141 -Ala F:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3E5Q)

(-) 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:202
 aligned with B8FW11_DESHD | B8FW11 from UniProtKB/TrEMBL  Length:232

    Alignment length:209
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         
         B8FW11_DESHD    18 NFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh......ee....eee........ee......eeeeeee...eeeeeeee................eeee...ee..eehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh-------.hhhhhhhhhhhhhhhh.ee..ee......hhhhhhhhh..hhhhhhhhhhhhhhhh.ee......ee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5q A  18 NFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQV-------PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
                                    27        37        47        57        67        77        87        97       107       117       127       137   |     - |     157       167       177       187       197       207       217         
                                                                                                                                                     141     149                                                                             

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with B8FW11_DESHD | B8FW11 from UniProtKB/TrEMBL  Length:232

    Alignment length:208
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
         B8FW11_DESHD    19 FFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhheeeee....eee........eeeeeeeeeeeeee.......eeeee....eee.......eeeeeeeeeeeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhh...eee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.....eee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5q B  19 FFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQV-------PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
                                    28        38        48        58        68        78        88        98       108       118       128       138  |      -|      158       168       178       188       198       208       218        
                                                                                                                                                    141     149                                                                             

Chain C from PDB  Type:PROTEIN  Length:203
 aligned with B8FW11_DESHD | B8FW11 from UniProtKB/TrEMBL  Length:232

    Alignment length:209
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         
         B8FW11_DESHD    18 NFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhheeeee....eee........eeee....eeeee........eeeee...eeee........eeeee...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------....hhhhhhhhhh...eee..eeee....hhhhhhhhhh...hhhhhhhhhhhhh..ee.....eee..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5q C  18 NFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVA------PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
                                    27        37        47        57        67        77        87        97       107       117       127       137    |    - |     157       167       177       187       197       207       217         
                                                                                                                                                      142    149                                                                             

Chain D from PDB  Type:PROTEIN  Length:201
 aligned with B8FW11_DESHD | B8FW11 from UniProtKB/TrEMBL  Length:232

    Alignment length:208
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
         B8FW11_DESHD    19 FFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhheeeee..............eeeee....eeeee........eee......eeee.......eeeee...eeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhh......eeee....hhhhhhhh..hhhhhhhhhhhhhh...ee....eeee..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5q D  19 FFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQV-------PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
                                    28        38        48        58        68        78        88        98       108       118       128       138  |      -|      158       168       178       188       198       208       218        
                                                                                                                                                    141     149                                                                             

Chain E from PDB  Type:PROTEIN  Length:203
 aligned with B8FW11_DESHD | B8FW11 from UniProtKB/TrEMBL  Length:232

    Alignment length:209
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         
         B8FW11_DESHD    18 NFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhheeeee....eee........eee.....eeeeee.....eeeeeee....eee.......eeeeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------hhhhhhhhhhhhhh...ee....eeee...hhhhhhhhh..hhhhhhhhhhhhhhh..eee...eeee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5q E  18 NFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVA------PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
                                    27        37        47        57        67        77        87        97       107       117       127       137    |    - |     157       167       177       187       197       207       217         
                                                                                                                                                      142    149                                                                             

Chain F from PDB  Type:PROTEIN  Length:203
 aligned with B8FW11_DESHD | B8FW11 from UniProtKB/TrEMBL  Length:232

    Alignment length:208
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
         B8FW11_DESHD    19 FFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhheeeee....eee.......eeeeeee..eeeee........eeeee....eeee.......eeeee...eeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....-----hhhhhhhhhhhhhhhh.eee..eee.....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e5q F  19 FFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAE-----PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLACLKRENILDKKKNKIIVYNLGELKHLS 226
                                    28        38        48        58        68        78        88        98       108       118       128       138    |    -|      158       168       178       188       198       208       218        
                                                                                                                                                      143   149                                                                             

   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  (0, 0)

(no "SCOP Domain" information available for 3E5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E5Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E5Q)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (B8FW11_DESHD | B8FW11)
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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  Cis Peptide Bonds
    Gln F:140 - Val F:141   [ RasMol ]  
    Val F:141 - Ala F:142   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        B8FW11_DESHD | B8FW113e5u 3e5x 3e6b 3e6c 3e6d

(-) Related Entries Specified in the PDB File

3e5u 3e5x 3e6b 3e6c 3e6d