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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND DPS FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  S. Roy, R. Saraswathi, D. Chatterji, M. Vijayan
Date :  13 Sep 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Dna-Binding Protein, Quarternary Assembly, Ferroxidation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Roy, R. Saraswathi, D. Chatterji, M. Vijayan
Structural Studies On The Second Mycobacterium Smegmatis Dps: Invariant And Variable Features Of Structure, Assembly And Function.
J. Mol. Biol. V. 375 948 2008
PubMed-ID: 18061613  |  Reference-DOI: 10.1016/J.JMB.2007.10.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STARVATION-INDUCIBLE DNA-BINDING PROTEIN OR FINE TANGLED PILI MAJOR SUBUNIT
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETMSDPS2
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MSMEG_3242
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: MC(2)155

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FE24Ligand/IonFE (II) ION
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE212Ligand/IonFE (II) ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:41 , ASP D:68 , GLU D:72BINDING SITE FOR RESIDUE FE2 D 162
2AC2SOFTWAREASP C:68 , GLU C:72 , HOH C:241 , HIS D:41BINDING SITE FOR RESIDUE FE2 C 162
3AC3SOFTWAREASN B:48 , ASP B:51 , ASN C:48 , ASP C:51 , ASN D:48 , ASP D:51BINDING SITE FOR RESIDUE MG D 163
4AC4SOFTWARELYS A:38 , HIS A:41 , ASP B:68 , GLU B:72 , HOH B:258BINDING SITE FOR RESIDUE FE2 B 162
5AC5SOFTWAREASP A:68 , GLU A:72 , HOH A:244 , LYS B:38 , HIS B:41BINDING SITE FOR RESIDUE FE2 A 162
6AC6SOFTWAREASN A:48 , ASP A:51BINDING SITE FOR RESIDUE MG A 163
7AC7SOFTWAREARG B:50 , ARG C:50 , HOH C:174 , ARG D:50BINDING SITE FOR RESIDUE CL B 163
8AC8SOFTWAREARG A:50 , HOH A:263BINDING SITE FOR RESIDUE CL A 164

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z90)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z90)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z90)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z90)

(-) 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:161
 aligned with A0QXB7_MYCS2 | A0QXB7 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         A0QXB7_MYCS2     1 MSARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
               SCOP domains d2z90a_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z90 A   1 MSARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with A0QXB7_MYCS2 | A0QXB7 from UniProtKB/TrEMBL  Length:161

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
         A0QXB7_MYCS2     2 SARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
               SCOP domains d2z90b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z90 B   2 SARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161


Chain C from PDB  Type:PROTEIN  Length:160
 aligned with A0QXB7_MYCS2 | A0QXB7 from UniProtKB/TrEMBL  Length:161

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
         A0QXB7_MYCS2     2 SARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
               SCOP domains d2z90c_ C: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z90 C   2 SARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161


Chain D from PDB  Type:PROTEIN  Length:161
 aligned with A0QXB7_MYCS2 | A0QXB7 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         A0QXB7_MYCS2     1 MSARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
               SCOP domains d2z90d_ D: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------Ferritin-2z90D01 D:21-160                                                                                                                   - Pfam domains (1)
           Pfam domains (2) --------------------Ferritin-2z90D02 D:21-160                                                                                                                   - Pfam domains (2)
           Pfam domains (3) --------------------Ferritin-2z90D03 D:21-160                                                                                                                   - Pfam domains (3)
           Pfam domains (4) --------------------Ferritin-2z90D04 D:21-160                                                                                                                   - Pfam domains (4)
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z90 D   1 MSARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLHGLIDGLEKQAWLIRSENRKV 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z90)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A0QXB7_MYCS2 | A0QXB7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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        A0QXB7_MYCS2 | A0QXB7: 4m32 4m33 4m34 4m35

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