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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CALCIUM CHELATING IMMUNODOMINANT ANTIGEN, CALCIUM DODECIN (RV0379),FROM MYCOBACTERIUM TUBERCULOSIS WITH A NOVEL CALCIUM-BINDING SITE
 
Authors :  A. Arulandu, J. C. Sacchettini
Date :  30 Aug 10  (Deposition) - 16 Mar 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Keywords :  Calcium Dodecin, Calcium Binding Protein, Dodecamer, Imuuno Dominant Antigen, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Arockiasamy, A. Aggarwal, C. G. Savva, A. Holzenburg, J. C. Sacchettini
Crystal Structure Of Calcium Dodecin (Rv0379), From Mycobacterium Tuberculosis With A Unique Calcium-Binding Site.
Protein Sci. V. 20 827 2011
PubMed-ID: 21370306  |  Reference-DOI: 10.1002/PRO.607

(-) Compounds

Molecule 1 - PROTEIN TRANSPORT PROTEIN SECE2
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RV0379, SECE2
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric/Biological Unit : ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FMT12Ligand/IonFORMIC ACID
3PT3Ligand/IonPLATINUM (II) ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:18 , HOH A:200 , GLU B:18 , HOH B:200 , GLU C:18BINDING SITE FOR RESIDUE CA A 72
02AC2SOFTWAREGLU A:42 , ASP A:44BINDING SITE FOR RESIDUE FMT A 73
03AC3SOFTWAREGLU B:42 , ASP B:44BINDING SITE FOR RESIDUE FMT B 72
04AC4SOFTWAREGLU C:42 , ASP C:44BINDING SITE FOR RESIDUE FMT C 72
05AC5SOFTWAREGLU D:18 , HOH D:200 , GLU E:18 , HOH E:200 , GLU F:18BINDING SITE FOR RESIDUE CA D 72
06AC6SOFTWAREGLU D:42 , ASP D:44BINDING SITE FOR RESIDUE FMT D 73
07AC7SOFTWAREASP E:44BINDING SITE FOR RESIDUE FMT E 72
08AC8SOFTWAREGLU F:42 , ASP F:44 , ARG F:56BINDING SITE FOR RESIDUE FMT F 72
09AC9SOFTWAREGLU G:18 , SER G:68 , HOH G:200 , GLU H:18 , GLU I:18BINDING SITE FOR RESIDUE CA G 72
10BC1SOFTWAREGLU G:42 , ASP G:44 , ARG G:56BINDING SITE FOR RESIDUE FMT G 73
11BC2SOFTWAREGLU H:42 , ASP H:44 , ARG H:56 , HOH H:226BINDING SITE FOR RESIDUE FMT H 72
12BC3SOFTWAREGLU I:42 , ASP I:44BINDING SITE FOR RESIDUE FMT I 72
13BC4SOFTWAREARG I:66 , HOH I:243 , GLN J:19BINDING SITE FOR RESIDUE PT I 73
14BC5SOFTWAREGLU J:18 , GLU K:18 , HOH K:200 , GLU L:18 , HOH L:200BINDING SITE FOR RESIDUE CA J 72
15BC6SOFTWAREASP J:44 , HOH J:227BINDING SITE FOR RESIDUE FMT J 73
16BC7SOFTWAREGLU K:42 , ASP K:44BINDING SITE FOR RESIDUE FMT K 72
17BC8SOFTWAREASP L:44 , HOH L:260BINDING SITE FOR RESIDUE FMT L 72

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro K:67 -Ser K:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ONR)

(-) 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:71
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:71
                                    10        20        30        40        50        60        70 
           DODEC_MYCTU    1 MSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3onr A  1 VSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    10        20        30        40        50        60        70 


Chain B from PDB  Type:PROTEIN  Length:70
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:70
                                    11        21        31        41        51        61        71
           DODEC_MYCTU    2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  3onr B  2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    11        21        31        41        51        61        71


Chain C from PDB  Type:PROTEIN  Length:70
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:70
                                    11        21        31        41        51        61        71
           DODEC_MYCTU    2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhh........................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  3onr C  2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    11        21        31        41        51        61        71


Chain D from PDB  Type:PROTEIN  Length:67
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:67
                                    11        21        31        41        51        61       
           DODEC_MYCTU    2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPA 68
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh...................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3onr D  2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPS 68
                                    11        21        31        41        51        61       


Chain E from PDB  Type:PROTEIN  Length:70
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:70
                                    11        21        31        41        51        61        71
           DODEC_MYCTU    2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  3onr E  2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    11        21        31        41        51        61        71


Chain F from PDB  Type:PROTEIN  Length:71
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:71
                                    10        20        30        40        50        60        70 
           DODEC_MYCTU    1 MSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3onr F  1 VSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    10        20        30        40        50        60        70 


Chain G from PDB  Type:PROTEIN  Length:71
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:71
                                    10        20        30        40        50        60        70 
           DODEC_MYCTU    1 MSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3onr G  1 VSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    10        20        30        40        50        60        70 


Chain H from PDB  Type:PROTEIN  Length:71
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:71
                                    10        20        30        40        50        60        70 
           DODEC_MYCTU    1 MSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhh......................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3onr H  1 VSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    10        20        30        40        50        60        70 


Chain I from PDB  Type:PROTEIN  Length:71
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:71
                                    10        20        30        40        50        60        70 
           DODEC_MYCTU    1 MSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhh......................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3onr I  1 VSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    10        20        30        40        50        60        70 


Chain J from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_MYCTU    2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQ 69
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhh..................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  3onr J  2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQ 69
                                    11        21        31        41        51        61        


Chain K from PDB  Type:PROTEIN  Length:67
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:67
                                    11        21        31        41        51        61       
           DODEC_MYCTU    2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPA 68
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhh.................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  3onr K  2 SVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPS 68
                                    11        21        31        41        51        61       


Chain L from PDB  Type:PROTEIN  Length:71
 aligned with DODEC_MYCTU | Q6MX43 from UniProtKB/Swiss-Prot  Length:71

    Alignment length:71
                                    10        20        30        40        50        60        70 
           DODEC_MYCTU    1 MSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPAQPR 71
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhh......................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3onr L  1 VSVYKVIDIIGTSPTSWEQAAAEAVQRARDSVDDIRVARVIEQDMAVDSAGKITYRIKLEVSFKMRPSQPL 71
                                    10        20        30        40        50        60        70
   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 3ONR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L   (DODEC_MYCTU | Q6MX43)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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