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The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with rrnA Sequence for the 23S rRNA and Genome-derived Sequences for r-Proteins
DOI:10.2210/pdb3cc2/pdb   NDB ID: RR0202
3CC2
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1484619.83
    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
    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
    1FFK  orignal data deposited in 2000 
    1S72  fully refined model of 1ffk structure factors 
    3CC4   
    3CC7   
    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: RR0202
     
 
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:   Gurel, G.,  Blaha, G.

    Deposition:   2008-02-23
    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]:   2.40
    R-Value: 0.199 (obs.)
    R-Free: 0.231
    Space Group: C 2 2 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 211.65 α = 90.00 
    b = 299.67 β = 90.00 
    c = 573.77 γ = 90.00