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(-) Description

Title :  X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DODECIN
 
Authors :  X. Vinzenz, W. Grosse, U. Linne, B. Meissner, L. -O. Essen
Date :  17 May 11  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Flavoprotein, Flavin Binding Protein, Protein-Engineering, Putative Storage Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Vinzenz, W. Grosse, U. Linne, B. Meissner, L. -O. Essen
Chemical Engineering Of Mycobacterium Tuberculosis Dodecin Hybrids.
Chem. Commun. (Camb. ) V. 47 11071 2011
PubMed-ID: 21897938  |  Reference-DOI: 10.1039/C1CC12929E

(-) Compounds

Molecule 1 - DODECIN
    Atcc: 25618
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-70
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2COA4Ligand/IonCOENZYME A
3FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL5Ligand/IonGLYCEROL
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (4, 42)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2COA12Ligand/IonCOENZYME A
3FMN12Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL15Ligand/IonGLYCEROL
5TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:34 , PHE A:64 , ARG A:65 , LEU A:66 , GLU A:67BINDING SITE FOR RESIDUE COA A1069
02AC2SOFTWAREHIS A:3 , TYR A:5 , ASP A:37 , TRP A:38 , ARG A:65 , HOH A:2051 , HOH A:2052 , GLN C:57 , FMN C:1070 , ARG D:45 , HIS D:47 , GLN D:57BINDING SITE FOR RESIDUE FMN A1070
03AC3SOFTWAREVAL A:7 , ILE A:8 , GLU A:9 , LYS A:61 , VAL C:7 , ILE C:8 , GLU C:9 , LYS C:61 , VAL D:7 , ILE D:8 , GLU D:9 , LYS D:61BINDING SITE FOR RESIDUE GOL A1071
04AC4SOFTWAREARG A:6 , ARG C:6 , ARG D:6BINDING SITE FOR RESIDUE GOL A1072
05AC5SOFTWAREVAL D:41BINDING SITE FOR RESIDUE GOL A1073
06AC6SOFTWAREARG B:34 , PHE B:64 , ARG B:65 , LEU B:66 , GLU B:67BINDING SITE FOR RESIDUE COA B1069
07AC7SOFTWAREARG A:45 , HIS A:47 , GLN A:57 , HIS B:3 , TYR B:5 , ASP B:37 , GLN B:57 , ARG B:65 , HOH B:2040 , HOH B:2068 , FMN D:1070BINDING SITE FOR RESIDUE FMN B1070
08AC8SOFTWAREVAL A:18 , ASP A:19 , HOH A:2026 , VAL B:18 , ASP B:19 , HOH B:2020 , VAL D:18 , ASP D:19BINDING SITE FOR RESIDUE GOL B1071
09AC9SOFTWAREVAL B:7 , GLU B:9 , LYS B:61BINDING SITE FOR RESIDUE GOL B1072
10BC1SOFTWAREARG B:6 , HOH B:2011BINDING SITE FOR RESIDUE CL B1073
11BC2SOFTWAREARG C:34 , PHE C:64 , ARG C:65 , LEU C:66 , GLU C:67BINDING SITE FOR RESIDUE COA C1069
12BC3SOFTWAREFMN A:1070 , HIS C:3 , TYR C:5 , ASP C:37 , ARG C:45 , HIS C:47 , GLN C:57 , ARG C:65 , HOH C:2034 , HOH C:2056 , GLN D:57BINDING SITE FOR RESIDUE FMN C1070
13BC4SOFTWAREVAL C:18 , ASP C:19 , HOH C:2057BINDING SITE FOR RESIDUE TRS C1071
14BC5SOFTWAREARG A:6 , ARG C:6 , ARG D:6 , HOH D:2010BINDING SITE FOR RESIDUE CL C1072
15BC6SOFTWAREARG D:34 , PHE D:64 , ARG D:65 , LEU D:66 , GLU D:67BINDING SITE FOR RESIDUE COA D1069
16BC7SOFTWAREGLN A:57 , ARG B:45 , HIS B:47 , GLN B:57 , FMN B:1070 , HIS D:3 , TYR D:5 , ASP D:37 , ARG D:65 , HOH D:2037 , HOH D:2038BINDING SITE FOR RESIDUE FMN D1070

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YIZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YIZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YIZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YIZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2YIZ)

(-) 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:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yiza_ A: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yiz A  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 68
                                    10        20        30        40        50        60        


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yizb_ B: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yiz B  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 68
                                    10        20        30        40        50        60        


Chain C from PDB  Type:PROTEIN  Length:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yizc_ C: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yiz C  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 68
                                    10        20        30        40        50        60        


Chain D from PDB  Type:PROTEIN  Length:68
 aligned with Q8VK10_MYCTO | Q8VK10 from UniProtKB/TrEMBL  Length:70

    Alignment length:68
                                    11        21        31        41        51        61        
          Q8VK10_MYCTO    2 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 69
               SCOP domains d2yizd_ D: automated matches                                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2yiz D  1 SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVTMKVGFRLED 68
                                    10        20        30        40        50        60
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YIZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YIZ)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8VK10_MYCTO | Q8VK10)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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        Q8VK10_MYCTO | Q8VK10: 2yj0 3oqt

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