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Structure of Thermus thermophilus 50S ribosome
DOI:10.2210/pdb4byc/pdb   NDB ID: NA2636
4BYC
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
4BYB   4BYC   4BYD   4BYE  
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The complete entry has been assigned PDB ID 4V8X and is available for download in PDBx/mmCIF and PDBML/XML formats from the FTP archive at:
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v8x.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v8x.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1403638.43
    Molecule: 50S RIBOSOMAL PROTEIN L27
    Polymer: 1 Type: protein Length: 85
    Chains: 0
    Organism: Thermus thermophilus HB8
    Gene Names: rpmA TTHA1782
    UniProtKB: Protein Feature View | Search PDB | P60493  
    Molecule: 50S RIBOSOMAL PROTEIN L28
    Polymer: 2 Type: protein Length: 98
    Chains: 1
    Organism: Thermus thermophilus HB8
    Gene Names: rpmB TTHA0042
    UniProtKB: Protein Feature View | Search PDB | P60494  
    Molecule: 50S RIBOSOMAL PROTEIN L29
    Polymer: 3 Type: protein Length: 72
    Chains: 2
    Organism: Thermus thermophilus HB8
    Gene Names: rpmC TTHA1684
    UniProtKB: Protein Feature View | Search PDB | Q5SHP6  
    Molecule: 50S RIBOSOMAL PROTEIN L30
    Polymer: 4 Type: protein Length: 60
    Chains: 3
    Organism: Thermus thermophilus HB8
    Gene Names: rpmD TTHA1674
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ6  
    Molecule: 50S RIBOSOMAL PROTEIN L31
    Polymer: 5 Type: protein Length: 71
    Chains: 4
    Organism: Thermus thermophilus HB8
    Gene Names: rpmE TTHA1073
    UniProtKB: Protein Feature View | Search PDB | Q5SJE1  
    Molecule: 50S RIBOSOMAL PROTEIN L32
    Polymer: 6 Type: protein Length: 60
    Chains: 5
    Organism: Thermus thermophilus HB8
    Gene Names: rpmF rpl32 TTHA0418
    UniProtKB: Protein Feature View | Search PDB | P80339  
    Molecule: 50S RIBOSOMAL PROTEIN L33
    Polymer: 7 Type: protein Length: 54
    Chains: 6
    Organism: Thermus thermophilus HB8
    Gene Names: rpmG rpl33 TTHA0250
    UniProtKB: Protein Feature View | Search PDB | P35871  
    Molecule: 50S RIBOSOMAL PROTEIN L34
    Polymer: 8 Type: protein Length: 49
    Chains: 7
    Organism: Thermus thermophilus HB8
    Gene Names: rpmH rpl34 TTHA0446
    UniProtKB: Protein Feature View | Search PDB | P80340  
    Molecule: 50S RIBOSOMAL PROTEIN L35
    Polymer: 9 Type: protein Length: 65
    Chains: 8
    Organism: Thermus thermophilus HB8
    Gene Names: rpmI TTHA0552
    UniProtKB: Protein Feature View | Search PDB | Q5SKU1  
    Molecule: 50S RIBOSOMAL PROTEIN L36
    Polymer: 10 Type: protein Length: 37
    Chains: 9
    Organism: Thermus thermophilus HB8
    Gene Names: rpmJ TTHA1668
    UniProtKB: Protein Feature View | Search PDB | Q5SHR2  
    Molecule: RNA (2848-MER)
    Polymer: 11 Type: rna Length: 2848
    Chains: A
    Organism: Thermus thermophilus HB8
    Molecule: RNA (119-MER)
    Polymer: 12 Type: rna Length: 119
    Chains: B
    Organism: Thermus thermophilus HB8
    Molecule: 50S RIBOSOMAL PROTEIN L1
    Polymer: 13 Type: protein Length: 229
    Chains: C
    Organism: Thermus thermophilus HB8
    Gene Names: rplA TTHA0246
    UniProtKB: Protein Feature View | Search PDB | Q5SLP7  
    Molecule: 50S RIBOSOMAL PROTEIN L2
    Polymer: 14 Type: protein Length: 276
    Chains: D
    Organism: Thermus thermophilus HB8
    Gene Names: rplB TTHA1689
    UniProtKB: Protein Feature View | Search PDB | P60405  
    Molecule: 50S RIBOSOMAL PROTEIN L3
    Polymer: 15 Type: protein Length: 206
    Chains: E
    Organism: Thermus thermophilus HB8
    Gene Names: rplC TTHA1692
    UniProtKB: Protein Feature View | Search PDB | Q5SHN8  
    Molecule: 50S RIBOSOMAL PROTEIN L4
    Polymer: 16 Type: protein Length: 210
    Chains: F
    Organism: Thermus thermophilus HB8
    Gene Names: rplD TTHA1691
    UniProtKB: Protein Feature View | Search PDB | Q5SHN9  
    Molecule: 50S RIBOSOMAL PROTEIN L5
    Polymer: 17 Type: protein Length: 182
    Chains: G
    Organism: Thermus thermophilus HB8
    Gene Names: rplE TTHA1680
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ0  
    Molecule: 50S RIBOSOMAL PROTEIN L6
    Polymer: 18 Type: protein Length: 180
    Chains: H
    Organism: Thermus thermophilus HB8
    Gene Names: rplF TTHA1677
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ3  
    Molecule: 50S RIBOSOMAL PROTEIN L9
    Polymer: 19 Type: protein Length: 148
    Chains: I
    Organism: Thermus thermophilus HB8
    Gene Names: rplI TTHA0242
    UniProtKB: Protein Feature View | Search PDB | Q5SLQ1  
    Molecule: 50S RIBOSOMAL PROTEIN L10
    Polymer: 20 Type: protein Length: 130
    Chains: J
    Organism: Thermus thermophilus HB8
    Molecule: 50S RIBOSOMAL PROTEIN L13
    Polymer: 21 Type: protein Length: 140
    Chains: N
    Organism: Thermus thermophilus HB8
    Gene Names: rplM TTHA1465
    UniProtKB: Protein Feature View | Search PDB | P60488  
    Molecule: 50S RIBOSOMAL PROTEIN L14
    Polymer: 22 Type: protein Length: 122
    Chains: O
    Organism: Thermus thermophilus HB8
    Gene Names: rplN TTHA1682
    UniProtKB: Protein Feature View | Search PDB | Q5SHP8  
    Molecule: 50S RIBOSOMAL PROTEIN L15
    Polymer: 23 Type: protein Length: 150
    Chains: P
    Organism: Thermus thermophilus HB8
    Gene Names: rplO TTHA1673
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ7  
    Molecule: 50S RIBOSOMAL PROTEIN L16
    Polymer: 24 Type: protein Length: 141
    Chains: Q
    Organism: Thermus thermophilus HB8
    Gene Names: rplP TTHA1685
    UniProtKB: Protein Feature View | Search PDB | P60489  
    Molecule: 50S RIBOSOMAL PROTEIN L17
    Polymer: 25 Type: protein Length: 118
    Chains: R
    Organism: Thermus thermophilus HB8
    Gene Names: rplQ rpl17 TTHA1663
    UniProtKB: Protein Feature View | Search PDB | Q9Z9H5  
    Molecule: 50S RIBOSOMAL PROTEIN L18
    Polymer: 26 Type: protein Length: 112
    Chains: S
    Organism: Thermus thermophilus HB8
    Gene Names: rplR TTHA1676
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ4  
    Molecule: 50S RIBOSOMAL PROTEIN L19
    Polymer: 27 Type: protein Length: 146
    Chains: T
    Organism: Thermus thermophilus HB8
    Gene Names: rplS TTHA1031
    UniProtKB: Protein Feature View | Search PDB | P60490  
    Molecule: 50S RIBOSOMAL PROTEIN L20
    Polymer: 28 Type: protein Length: 118
    Chains: U
    Organism: Thermus thermophilus HB8
    Gene Names: rplT TTHA0553
    UniProtKB: Protein Feature View | Search PDB | P60491  
    Molecule: 50S RIBOSOMAL PROTEIN L21
    Polymer: 29 Type: protein Length: 101
    Chains: V
    Organism: Thermus thermophilus HB8
    Gene Names: rplU TTHA1783
    UniProtKB: Protein Feature View | Search PDB | P60492  
    Molecule: 50S RIBOSOMAL PROTEIN L22
    Polymer: 30 Type: protein Length: 113
    Chains: W
    Organism: Thermus thermophilus HB8
    Gene Names: rplV TTHA1687
    UniProtKB: Protein Feature View | Search PDB | Q5SHP3  
    Molecule: 50S RIBOSOMAL PROTEIN L23
    Polymer: 31 Type: protein Length: 96
    Chains: X
    Organism: Thermus thermophilus HB8
    Gene Names: rplW TTHA1690
    UniProtKB: Protein Feature View | Search PDB | Q5SHP0  
    Molecule: 50S RIBOSOMAL PROTEIN L24
    Polymer: 32 Type: protein Length: 110
    Chains: Y
    Organism: Thermus thermophilus HB8
    Gene Names: rplX TTHA1681
    UniProtKB: Protein Feature View | Search PDB | Q5SHP9  
    Molecule: 50S RIBOSOMAL PROTEIN L25
    Polymer: 33 Type: protein Length: 206
    Chains: Z
    Organism: Thermus thermophilus HB8
    Gene Names: rplY rpl25 rptL5 TTHA1589
    UniProtKB: Protein Feature View | Search PDB | Q5SHZ1  
     
  •   Structure Validation Hide

    Download full validation report    

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 2
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 3
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 4
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 5
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 6
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 7
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 8
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 9
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 10
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 11
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 12
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 13
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 14
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 15
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 16
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 17
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 18
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 19
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 20
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 21
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 22
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 23
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 24
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 25
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 26
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 27
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 28
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 29
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 30
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 31
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 32
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 33
    Scientific Name: Thermus thermophilus   Taxonomy    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    UNK
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    UNK C4 H9 N O2 lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2636
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (4BYB and 4BYC)
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Feng, S.,  Chen, Y.,  Kamada, K.,  Wang, H.,  Tang, K.,  Wang, M.,  Gao, Y.G.

    Deposition:   2013-07-19
    Release:   2013-08-28
    Last Modified (REVDAT):   2013-12-25
     
  •   Revision History    Hide
    Mouse over text for details
    2013-12-25
    Other
    2013-12-25
    Biological assembly
    2013-12-25
    Linkage
    2013-12-25
    Atom nomenclature
    2013-11-13
    Citation
    2013-09-18
    Entry title
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.35
    R-Value: 0.223 (obs.)
    R-Free: 0.261
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 211.59 α = 90.00 
    b = 455.43 β = 90.00 
    c = 616.94 γ = 90.00