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(-) Description

Title :  CRYSTAL STRUCTURE OF GATED-PORE MUTANT H141D OF SECOND DNA-BINDING PROTEIN UNDER STARVATION FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  S. M. Williams, A. V. Chandran, M. S. Vijayabaskar, S. Roy, H. Balaram, S. Vishveshwara, M. Vijayan, D. Chatterji
Date :  06 Aug 13  (Deposition) - 05 Mar 14  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Ferritin-Like Fold, Ferroxidation, Iron, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Williams, A. V. Chandran, M. S. Vijayabaskar, S. Roy, H. Balaram, S. Vishveshwara, M. Vijayan, D. Chatterji
A Histidine Aspartate Ionic Lock Gates The Iron Passage In Miniferritins From Mycobacterium Smegmatis
J. Biol. Chem. V. 289 11042 2014
PubMed-ID: 24573673  |  Reference-DOI: 10.1074/JBC.M113.524421

(-) Compounds

Molecule 1 - PUTATIVE STARVATION-INDUCED DNA PROTECTING PROTEIN/FERRITIN AND DPS
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DPS2, MSMEG_3242, MSMEI_3159
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155
    Synonym: STARVATION-INDUCIBLE DNA-BINDING PROTEIN OR FINE TANGLED PILI MAJOR SUBUNIT

 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, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FE24Ligand/IonFE (II) ION
3MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FE212Ligand/IonFE (II) ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:68 , GLU A:72 , HIS B:41 , ASP B:57BINDING SITE FOR RESIDUE FE2 A 201
02AC2SOFTWAREASN A:48 , ASP A:51BINDING SITE FOR RESIDUE MG A 202
03AC3SOFTWAREASP A:138 , HOH A:392 , HOH A:393 , ASP B:138 , ASP C:138 , HOH C:390BINDING SITE FOR RESIDUE MG A 203
04AC4SOFTWAREARG A:50 , HOH A:389BINDING SITE FOR RESIDUE CL A 204
05AC5SOFTWAREHIS A:41 , ASP A:57 , HOH A:404 , ASP B:68 , GLU B:72 , HOH B:370BINDING SITE FOR RESIDUE FE2 B 201
06AC6SOFTWAREASN B:48 , ASP B:51 , ASN C:48 , ASP C:51 , ASN D:48 , ASP D:51BINDING SITE FOR RESIDUE MG B 202
07AC7SOFTWAREHOH A:394 , HOH A:396 , HOH B:371 , HOH C:302 , HOH C:391BINDING SITE FOR RESIDUE MG B 203
08AC8SOFTWAREARG B:50 , ARG C:50 , HOH C:388 , ARG D:50BINDING SITE FOR RESIDUE CL B 204
09AC9SOFTWAREASP C:68 , GLU C:72 , HOH C:396 , HIS D:41 , ASP D:57BINDING SITE FOR RESIDUE FE2 C 201
10BC1SOFTWAREHIS C:41 , ASP C:57 , ASP D:68 , GLU D:72BINDING SITE FOR RESIDUE FE2 D 201
11BC2SOFTWAREASP D:138 , HOH D:370BINDING SITE FOR RESIDUE MG D 202
12BC3SOFTWAREHOH D:369 , HOH D:373BINDING SITE FOR RESIDUE MG D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M33)

(-) Exons   (0, 0)

(no "Exon" information available for 4M33)

(-) 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
                                                                                                                                                                                                 
               SCOP domains d4m33a_ 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
                 4m33 A   1 MSARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLDGLIDGLEKQAWLIRSENRKV 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
                                                                                                                                                                                                
               SCOP domains d4m33b_ 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
                 4m33 B   2 SARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLDGLIDGLEKQAWLIRSENRKV 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
                                                                                                                                                                                                
               SCOP domains d4m33c_ 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
                 4m33 C   2 SARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLDGLIDGLEKQAWLIRSENRKV 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
                                                                                                                                                                                                 
               SCOP domains d4m33d_ D: 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
                 4m33 D   1 MSARRTESDIQGFHATPEFGGNLQKVLVDLIELSLQGKQAHWNVVGSNFRDLHLQLDELVDFAREGSDTIAERMRALDAVPDGRSDTVAATTTLPEFPAFERSTADVVDLITTRINATVDTIRRVHDAVDAEDPSTADLLDGLIDGLEKQAWLIRSENRKV 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)
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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  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M33)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M33)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        A0QXB7_MYCS2 | A0QXB7: 2z90 4m32 4m34 4m35

(-) Related Entries Specified in the PDB File

4m32 4m34 4m35