2ZJR

Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans

Structural Biology Knowledgebase: 2ZJR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.311
  • R-Value Work: 0.277

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZJR

Classification: RIBOSOME

Total Structure Weight: 1365293.41


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2 A 274 Deinococcus radiodurans Gene Name(s): rplB DR_0314
50S ribosomal protein L3 B 211 Deinococcus radiodurans Gene Name(s): rplC DR_0311
50S ribosomal protein L4 C 205 Deinococcus radiodurans Gene Name(s): rplD DR_0312
50S ribosomal protein L5 D 180 Deinococcus radiodurans Gene Name(s): rplE DR_0323
50S ribosomal protein L6 E 185 Deinococcus radiodurans Gene Name(s): rplF DR_2111
50S ribosomal protein L11 F 144 Deinococcus radiodurans Gene Name(s): rplK DR_2046
50S ribosomal protein L13 G 174 Deinococcus radiodurans Gene Name(s): rplM DR_0174
50S ribosomal protein L14 H 134 Deinococcus radiodurans Gene Name(s): rplN DR_0321
50S ribosomal protein L15 I 156 Deinococcus radiodurans Gene Name(s): rplO DR_2115
50S ribosomal protein L16 J 142 Deinococcus radiodurans Gene Name(s): rplP DR_0318
50S ribosomal protein L17 K 116 Deinococcus radiodurans Gene Name(s): rplQ DR_2129
50S ribosomal protein L18 L 114 Deinococcus radiodurans Gene Name(s): rplR DR_2112
50S ribosomal protein L19 M 166 Deinococcus radiodurans Gene Name(s): rplS DR_0755
50S ribosomal protein L20 N 118 Deinococcus radiodurans Gene Name(s): rplT DR_2004
50S ribosomal protein L21 O 100 Deinococcus radiodurans Gene Name(s): rplU DR_0086
50S ribosomal protein L22 P 134 Deinococcus radiodurans Gene Name(s): rplV DR_0316
50S ribosomal protein L23 Q 95 Deinococcus radiodurans Gene Name(s): rplW DR_0313
50S ribosomal protein L24 R 115 Deinococcus radiodurans Gene Name(s): rplX DR_0322
50S ribosomal protein L25 S 237 Deinococcus radiodurans Gene Name(s): rplY ctc DR_0427
50S ribosomal protein L27 T 91 Deinococcus radiodurans Gene Name(s): rpmA DR_0085
50S ribosomal protein L28 U 81 Deinococcus radiodurans Gene Name(s): rpmB DR_2524
50S ribosomal protein L29 V 67 Deinococcus radiodurans Gene Name(s): rpmC DR_0319
50S ribosomal protein L30 W 55 Deinococcus radiodurans Gene Name(s): rpmD DR_2114
50S ribosomal protein L32 Z 60 Deinococcus radiodurans Gene Name(s): rpmF DR_2366
50S ribosomal protein L33 1 55 Deinococcus radiodurans Gene Name(s): rpmG DR_2049
50S ribosomal protein L34 2 47 Deinococcus radiodurans Gene Name(s): rpmH DR_2152
50S ribosomal protein L35 3 66 Deinococcus radiodurans Gene Name(s): rpmI DR_2005
50S ribosomal protein L36 4 37 Deinococcus radiodurans Gene Name(s): rpmJ DR_2124
Macromolecule Entities
Molecule Chains Length Organism Details
ribosomal 23S RNA X 2880 Deinococcus radiodurans
ribosomal 5S RNA Y 123 Deinococcus radiodurans

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

X, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.311
  • R-Value Work: 0.277
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 169.90 α = 90.00
b = 408.90 β = 90.00
c = 694.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-08
  • Released Date: 2008-06-17
  • Deposition author(s): Harms, J.M., Wilson, D.N., Schluenzen, F., Connell, S.R., Stachelhaus, T., Zaborowska, Z., Spahn, C.M.T., Fucini, P.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4