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(-) Description

Title :  CRYSTAL STRUCTURE OF RTX DOMAIN BLOCK V OF ADENYLATE CYCLASE TOXIN FROM BORDETELLA PERTUSSIS
 
Authors :  L. Motlova, C. Barinka, L. Bumba
Date :  29 Jul 15  (Deposition) - 02 Sep 15  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Adenylate Cyclase, Rtx Motifs, Calcium Binding, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Bumba, J. Masin, P. Macek, T. Wald, L. Motlova, I. Bibova, N. Klimova L. Bednarova, V. Veverka, M. Kachala, D. I. Svergun, C. Barinka, P. Seb
Calcium-Driven Folding Of Rtx Domain Beta-Rolls Ratchets Translocation Of Rtx Proteins Through Type I Secretion Ducts.
Mol. Cell V. 62 47 2016
PubMed-ID: 27058787  |  Reference-DOI: 10.1016/J.MOLCEL.2016.03.018

(-) Compounds

Molecule 1 - BIFUNCTIONAL HEMOLYSIN/ADENYLATE CYCLASE
    Chains: A, B
    EC Number: 4.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET42B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BLOCK V OF RTX DOMAIN (UNP RESISDUES 1529-1681)
    Gene: CYA, CYAA, BP0760
    Organism Scientific: BORDETELLA PERTUSSIS (STRAIN TOHAMA I / ATCC BAA-589 / NCTC 13251)
    Organism Taxid: 257313
    Other Details: THE LAST 5 AMINO ACIDS ARE TOO FLEXIBLE TO BE FIT IN THE ELECTRON DENSITY MAP.
    Strain: TOHAMA I / ATCC BAA-589 / NCTC 13251
    Synonym: AC-HLY,ACT,CYCLOLYSIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1CA16Ligand/IonCALCIUM ION
2NO32Ligand/IonNITRATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NO31Ligand/IonNITRATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NO31Ligand/IonNITRATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:1539 , GLY A:1541 , ASN A:1543 , GLY A:1556 , ALA A:1558 , ASP A:1561binding site for residue CA A 1701
02AC2SOFTWAREGLY A:1557 , GLY A:1559 , ASP A:1561 , GLY A:1574 , ALA A:1576 , ASP A:1579binding site for residue CA A 1702
03AC3SOFTWAREASP A:1575 , GLY A:1577 , ASP A:1579 , TYR A:1596 , ASP A:1599binding site for residue CA A 1703
04AC4SOFTWARESER A:1530 , ARG A:1532 , ASP A:1534 , GLY A:1547 , ALA A:1549 , ASP A:1552binding site for residue CA A 1704
05AC5SOFTWARELEU A:1548 , GLY A:1550 , ASP A:1552 , GLY A:1565 , GLU A:1567 , ASP A:1570binding site for residue CA A 1705
06AC6SOFTWAREASP A:1566 , GLY A:1568 , ASP A:1570 , GLY A:1583 , GLN A:1585 , ASP A:1588binding site for residue CA A 1706
07AC7SOFTWAREGLY A:1584 , GLY A:1586 , ASP A:1588 , GLU A:1603 , GLY A:1605 , ASP A:1609binding site for residue CA A 1707
08AC8SOFTWAREGLY A:1606 , ASP A:1609 , ARG A:1652 , GLU A:1654 , HOH A:1824 , HOH A:1829binding site for residue CA A 1708
09AC9SOFTWAREGLU A:1567 , GLN A:1585 , HOH A:1826 , HOH A:1837 , HOH A:1847 , HOH A:1870 , GLU B:1567 , GLN B:1585binding site for residue NO3 A 1709
10AD1SOFTWAREGLY A:1529 , ASN A:1546 , LEU A:1548 , HIS B:1643 , HIS B:1651 , HOH B:1841 , HOH B:1848binding site for residue NO3 B 1701
11AD2SOFTWAREASP B:1539 , GLY B:1541 , ASN B:1543 , GLY B:1556 , ALA B:1558 , ASP B:1561binding site for residue CA B 1702
12AD3SOFTWAREGLY B:1557 , GLY B:1559 , ASP B:1561 , GLY B:1574 , ALA B:1576 , ASP B:1579binding site for residue CA B 1703
13AD4SOFTWAREASP B:1575 , GLY B:1577 , ASP B:1579 , TYR B:1596 , ASP B:1599binding site for residue CA B 1704
14AD5SOFTWARESER B:1530 , ARG B:1532 , ASP B:1534 , GLY B:1547 , ALA B:1549 , ASP B:1552binding site for residue CA B 1705
15AD6SOFTWARELEU B:1548 , GLY B:1550 , ASP B:1552 , GLY B:1565 , GLU B:1567 , ASP B:1570binding site for residue CA B 1706
16AD7SOFTWAREASP B:1566 , GLY B:1568 , ASP B:1570 , GLY B:1583 , GLN B:1585 , ASP B:1588binding site for residue CA B 1707
17AD8SOFTWAREGLY B:1584 , GLY B:1586 , ASP B:1588 , GLU B:1603 , GLY B:1605 , ASP B:1609binding site for residue CA B 1708
18AD9SOFTWAREGLY B:1606 , ASP B:1609 , ARG B:1652 , GLU B:1654 , HOH B:1825 , HOH B:1853binding site for residue CA B 1709

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CXL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CXL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CXL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CXL)

(-) Exons   (0, 0)

(no "Exon" information available for 5CXL)

(-) 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:148
                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eee......eee......eee......eee......eee......eeeee....eeee........eeeee.hhh.eeeeee..eeeeee.....eeee.....hhhhh..eeee..eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cxl A 1529 GSARDDVLIGDAGANVLNGLAGNDVLSGGAGDDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMA 1676
                                  1538      1548      1558      1568      1578      1588      1598      1608      1618      1628      1638      1648      1658      1668        


Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eee......eee......eee......eee......eee......eeeee....eeee........eeeee.hhh.eeeeee..eeeeee.....eeee.....hhhhh..eeee..eeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cxl B 1529 GSARDDVLIGDAGANVLNGLAGNDVLSGGAGDDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMA 1676
                                  1538      1548      1558      1568      1578      1588      1598      1608      1618      1628      1638      1648      1658      1668
   Legend:   → Mismatch (orange background)
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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 5CXL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CXL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CXL)

(-) Gene Ontology  (14, 14)

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        CYAA_BORPE | P0DKX7: 1yrt 1yru 1zot 2col

(-) Related Entries Specified in the PDB File

5cvw THE SAME PROTEIN IN DIFFERENT SPACE GROUP WITH TWO MOLECULES IN ASYMETRIC UNIT.