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Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B. This file contains the 30S subunit of the first 70S ribosome, with hygromycin B bound. The entire crystal structure contains two 70S ribosomes.
 
 
DOI:10.2210/pdb3df1/pdb   NDB ID: RR0228
3DF1
 
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
3DF1   3DF2   3DF3   3DF4  
Download All Files   
 
 
 
Primary Citation
spinning wheel
 
 
  •  
    Move Section Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 789558.49
     
    Molecule:16S ribosomal RNA
    Polymer:1Type:polyribonucleotideLength:1542
    Chains:A
    Molecule:30S ribosomal protein S3
    Polymer:2Type:polypeptide(L)Length:232
    Chains:C
    Molecule:30S ribosomal protein S4
    Polymer:3Type:polypeptide(L)Length:205
    Chains:D
    Molecule:30S ribosomal protein S5
    Polymer:4Type:polypeptide(L)Length:166
    Chains:E
    Molecule:30S ribosomal protein S6
    Polymer:5Type:polypeptide(L)Length:135
    Chains:F
    Molecule:30S ribosomal protein S7
    Polymer:6Type:polypeptide(L)Length:178
    Chains:G
    Molecule:30S ribosomal protein S8
    Polymer:7Type:polypeptide(L)Length:129
    Chains:H
    Molecule:30S ribosomal protein S9
    Polymer:8Type:polypeptide(L)Length:129
    Chains:I
    Molecule:30S ribosomal protein S10
    Polymer:9Type:polypeptide(L)Length:103
    Chains:J
    Molecule:30S ribosomal protein S11
    Polymer:10Type:polypeptide(L)Length:128
    Chains:K
    Molecule:30S ribosomal protein S12
    Polymer:11Type:polypeptide(L)Length:123
    Chains:L
    Molecule:30S ribosomal protein S13
    Polymer:12Type:polypeptide(L)Length:117
    Chains:M
    Molecule:30S ribosomal protein S14
    Polymer:13Type:polypeptide(L)Length:100
    Chains:N
    Molecule:30S ribosomal protein S15
    Polymer:14Type:polypeptide(L)Length:89
    Chains:O
    Molecule:30S ribosomal protein S16
    Polymer:15Type:polypeptide(L)Length:82
    Chains:P
    Molecule:30S ribosomal protein S17
    Polymer:16Type:polypeptide(L)Length:83
    Chains:Q
    Molecule:30S ribosomal protein S18
    Polymer:17Type:polypeptide(L)Length:74
    Chains:R
    Molecule:30S ribosomal protein S19
    Polymer:18Type:polypeptide(L)Length:91
    Chains:S
    Molecule:30S ribosomal protein S20
    Polymer:19Type:polypeptide(L)Length:86
    Chains:T
    Molecule:30S ribosomal protein S2
    Polymer:20Type:polypeptide(L)Length:240
    Chains:B
    Molecule:30S ribosomal protein S21
    Polymer:21Type:polypeptide(L)Length:71
    Chains:U
     
     
  •  
    Move Section Source Hide
    Polymer: 1
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 2
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 3
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 4
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 5
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 6
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 7
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 8
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 9
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 10
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 11
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 12
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 13
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 14
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 15
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 16
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 17
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 18
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 19
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 20
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
    Polymer: 21
    Scientific Name: Escherichia coli Go to NCBI Taxonomy entry  
     
     
  •  
    Move Section Ligand Chemical Component Hide
    Identifier Name Formula Interaction View Links
    HYG     HYGROMYCIN B C20 H37 N3 O13 3DLigand Explorer Link out to Ligand Expos:HYG Link out to SuperLigands:HYG Link out to SuperHapten:HYG
    MG     MAGNESIUM ION Mg 3DLigand Explorer Link out to Ligand Expos:MG Link out to SuperLigands:MG Link out to SuperHapten:MG
     
     
  •  
    Move Section Derived Data Hide
     
     
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< Biological Assembly 1    Help >
View in Jmol
Composite of PDB entries (3DF1 and 3DF2)
 
 
 
  •  
    Move Section Deposition Summary Hide
    Authors:   Borovinskaya, M.A.,   Shoji, S.,   Fredrick, K.,   Cate, J.H.D.

    Deposition:   2008-06-11
    Release:   2008-08-19
    Last Modified (REVDAT):   2009-11-03
     
     
  •  
    Move Section Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Experimental Data:   Download Structure Factors
    View a histogram of Resolution Resolution[Å]: 3.50
    R-Value: 0.269 (work)
    R-Free: 0.318
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 208.70 α = 90.00 
    b = 379.50 β = 90.00 
    c = 739.30 γ = 90.00