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Structure of Anisomycin resistant 50S Ribosomal Subunit: 23S rRNA mutation C2487U
DOI:10.2210/pdb3cc7/pdb   NDB ID: RR0204
3CC7
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1493255.89
    Molecule: 50S ribosomal protein L2P
    Polymer: 1 Type: protein Length: 240
    Chains: A
    Organism: Haloarcula marismortui
    Gene Names: rpl2 rrnAC1608
    UniProtKB: Protein Feature View | Search PDB | P20276  
    Molecule: 50S ribosomal protein L3P
    Polymer: 2 Type: protein Length: 338
    Chains: B
    Organism: Haloarcula marismortui
    Gene Names: rpl3 rrnAC1611
    UniProtKB: Protein Feature View | Search PDB | P20279  
    Molecule: 50S ribosomal protein L4P
    Polymer: 3 Type: protein Length: 246
    Chains: C
    Organism: Haloarcula marismortui
    Gene Names: rpl4 rrnAC1610
    UniProtKB: Protein Feature View | Search PDB | P12735  
    Molecule: 50S ribosomal protein L5P
    Polymer: 4 Type: protein Length: 177
    Chains: D
    Organism: Haloarcula marismortui
    Gene Names: rpl5 rrnAC1598
    UniProtKB: Protein Feature View | Search PDB | P14124  
    Molecule: 50S ribosomal protein L6P
    Polymer: 5 Type: protein Length: 178
    Chains: E
    Organism: Haloarcula marismortui
    Gene Names: rpl6 rrnAC1596
    UniProtKB: Protein Feature View | Search PDB | P14135  
    Molecule: 50S ribosomal protein L7Ae
    Polymer: 6 Type: protein Length: 120
    Chains: F
    Organism: Haloarcula marismortui
    Gene Names: rpl7ae rrnAC0103
    UniProtKB: Protein Feature View | Search PDB | P12743  
    Molecule: 50S ribosomal protein L10E
    Polymer: 7 Type: protein Length: 348
    Chains: G
    Organism: Haloarcula marismortui
    Gene Names: rpl10 rpl10e rplP0 rrnAC1417
    UniProtKB: Protein Feature View | Search PDB | P15825  
    Molecule: 50S ribosomal protein L10e
    Polymer: 8 Type: protein Length: 177
    Chains: H
    Organism: Haloarcula marismortui
    Gene Names: rpl10e rrnAC2357
    UniProtKB: Protein Feature View | Search PDB | P60617  
    Molecule: 50S ribosomal protein L11P
    Polymer: 9 Type: protein Length: 162
    Chains: I
    Organism: Haloarcula marismortui
    Gene Names: rpl11 rrnAC1414
    UniProtKB: Protein Feature View | Search PDB | P14122  
    Molecule: 50S ribosomal protein L13P
    Polymer: 10 Type: protein Length: 145
    Chains: J
    Organism: Haloarcula marismortui
    Gene Names: rpl13 rrnAC0065
    UniProtKB: Protein Feature View | Search PDB | P29198  
    Molecule: 50S ribosomal protein L14P
    Polymer: 11 Type: protein Length: 132
    Chains: K
    Organism: Haloarcula marismortui
    Gene Names: rpl14 rrnAC1602
    UniProtKB: Protein Feature View | Search PDB | P22450  
    Molecule: 50S ribosomal protein L15P
    Polymer: 12 Type: protein Length: 165
    Chains: L
    Organism: Haloarcula marismortui
    Gene Names: rpl15p rrnAC1590
    UniProtKB: Protein Feature View | Search PDB | P12737  
    Molecule: 50S ribosomal protein L15e
    Polymer: 13 Type: protein Length: 196
    Chains: M
    Organism: Haloarcula marismortui
    Gene Names: rpl15e rrnAC2065
    UniProtKB: Protein Feature View | Search PDB | P60618  
    Molecule: 50S ribosomal protein L18P
    Polymer: 14 Type: protein Length: 187
    Chains: N
    Organism: Haloarcula marismortui
    Gene Names: rpl18p rrnAC1593
    UniProtKB: Protein Feature View | Search PDB | P14123  
    Molecule: 50S ribosomal protein L18e
    Polymer: 15 Type: protein Length: 116
    Chains: O
    Organism: Haloarcula marismortui
    Gene Names: rpl18e rrnAC0064
    UniProtKB: Protein Feature View | Search PDB | P12733  
    Molecule: 50S ribosomal protein L19e
    Polymer: 16 Type: protein Length: 149
    Chains: P
    Organism: Haloarcula marismortui
    Gene Names: rpl19e rrnAC1594
    UniProtKB: Protein Feature View | Search PDB | P14119  
    Molecule: 50S ribosomal protein L21e
    Polymer: 17 Type: protein Length: 96
    Chains: Q
    Organism: Haloarcula marismortui
    Gene Names: rpl21e rrnAC0260
    UniProtKB: Protein Feature View | Search PDB | P12734  
    Molecule: 50S ribosomal protein L22P
    Polymer: 18 Type: protein Length: 155
    Chains: R
    Organism: Haloarcula marismortui
    Gene Names: rpl22p rrnAC1606
    UniProtKB: Protein Feature View | Search PDB | P10970  
    Molecule: 50S ribosomal protein L23P
    Polymer: 19 Type: protein Length: 85
    Chains: S
    Organism: Haloarcula marismortui
    Gene Names: rpl23p rrnAC1609
    UniProtKB: Protein Feature View | Search PDB | P12732  
    Molecule: 50S ribosomal protein L24P
    Polymer: 20 Type: protein Length: 120
    Chains: T
    Organism: Haloarcula marismortui
    Gene Names: rpl24p rrnAC1601
    UniProtKB: Protein Feature View | Search PDB | P10972  
    Molecule: 50S ribosomal protein L24e
    Polymer: 21 Type: protein Length: 67
    Chains: U
    Organism: Haloarcula marismortui
    Gene Names: rpl24e rrnAC0104
    UniProtKB: Protein Feature View | Search PDB | P14116  
    Molecule: 50S ribosomal protein L29P
    Polymer: 22 Type: protein Length: 71
    Chains: V
    Organism: Haloarcula marismortui
    Gene Names: rpl29p rrnAC1604
    UniProtKB: Protein Feature View | Search PDB | P10971  
    Molecule: 50S ribosomal protein L30P
    Polymer: 23 Type: protein Length: 154
    Chains: W
    Organism: Haloarcula marismortui
    Gene Names: rpl30p rrnAC1591
    UniProtKB: Protein Feature View | Search PDB | P14121  
    Molecule: 50S ribosomal protein L31e
    Polymer: 24 Type: protein Length: 92
    Chains: X
    Organism: Haloarcula marismortui
    Gene Names: rpl31e rrnAC3113
    UniProtKB: Protein Feature View | Search PDB | P18138  
    Molecule: 50S ribosomal protein L32e
    Polymer: 25 Type: protein Length: 241
    Chains: Y
    Organism: Haloarcula marismortui
    Gene Names: rpl32e rrnAC1595
    UniProtKB: Protein Feature View | Search PDB | P12736  
    Molecule: 50S ribosomal protein L37Ae
    Polymer: 26 Type: protein Length: 116
    Chains: Z
    Organism: Haloarcula marismortui
    Gene Names: rpl37ae rrnAC1669
    UniProtKB: Protein Feature View | Search PDB | P60619  
    Molecule: 50S ribosomal protein L37e
    Polymer: 27 Type: protein Length: 57
    Chains: 1
    Organism: Haloarcula marismortui
    Gene Names: rpl37e rrnAC0797.1
    UniProtKB: Protein Feature View | Search PDB | P32410  
    Molecule: 50S ribosomal protein L39e
    Polymer: 28 Type: protein Length: 50
    Chains: 2
    Organism: Haloarcula marismortui
    Gene Names: rpl39e rrnAC3112
    UniProtKB: Protein Feature View | Search PDB | P22452  
    Molecule: 50S ribosomal protein L44E
    Polymer: 29 Type: protein Length: 92
    Chains: 3
    Organism: Haloarcula marismortui
    Gene Names: rpl44e rrnAC3514
    UniProtKB: Protein Feature View | Search PDB | P32411  
    Molecule: 23S ribosomal RNA
    Polymer: 30 Type: rna Length: 2923
    Chains: 0
    Mutation: G2099A, C2487U
    Organism: Haloarcula marismortui
    Molecule: 5S ribosomal RNA
    Polymer: 31 Type: rna Length: 122
    Chains: 9
    Organism: Haloarcula marismortui
     
  •   Structure Validation Hide

    Download full validation report    

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 2
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 3
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 4
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 5
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 6
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 7
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 8
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 9
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 10
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 11
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 12
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 13
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 14
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 15
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 16
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 17
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 18
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 19
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 20
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 21
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 22
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 23
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 24
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 25
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 26
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 27
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 28
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 29
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 30
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
    Polymer: 31
    Scientific Name: Haloarcula marismortui   Taxonomy   Common Name: Halobacterium marismortui  
     
  •   Related PDB Entries Hide
    Identifier Details
    3CC2  Starting model for refinement 
    3CC4   
    3CCE   
    3CCJ   
    3CCL   
    3CCM   
    3CCQ   
    3CCR   
    3CCS   
    3CCU   
    3CCV   
    3CD6   
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    1MA
    Search 
    1MA C11 H16 N5 O7 P A rnaLinking
    OMU
    Search 
    OMU C10 H15 N2 O9 P U rnaLinking
    OMG
    Search 
    OMG C11 H16 N5 O8 P G rnaLinking
    UR3
    Search 
    UR3 C10 H15 N2 O9 P U rnaLinking
    PSU
    Search 
    PSU C9 H13 N2 O9 P U rnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: RR0204
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
Downloadable viewers:
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Blaha, G.,  Gurel, G.

    Deposition:   2008-02-25
    Release:   2008-05-20
    Last Modified (REVDAT):   2014-05-14
     
  •   Revision History    Hide
    Mouse over text for details
    2014-05-14
    Other
    2011-07-13
    Non-polymer description
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.70
    R-Value: 0.184 (work)
    R-Free: 0.226
    Space Group: C 2 2 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 212.83 α = 90.00 
    b = 299.90 β = 90.00 
    c = 576.01 γ = 90.00