1JJ2

Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution

Structural Biology Knowledgebase: 1JJ2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1JJ2

Classification: RIBOSOME

Total Structure Weight: 1458161.25


Macromolecule Entities
Molecule Chains Length Organism Details
RIBOSOMAL PROTEIN L2 A 239 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
RIBOSOMAL PROTEIN L3 B 337 Haloarcula marismortui Mutation: ΔP310, F310R
Gene Name(s): rpl3 rrnAC1611
RIBOSOMAL PROTEIN L4 C 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
RIBOSOMAL PROTEIN L5 D 176 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
RIBOSOMAL PROTEIN L6 E 177 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
RIBOSOMAL PROTEIN L7AE F 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
RIBOSOMAL PROTEIN L10 G 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
RIBOSOMAL PROTEIN L10E H 167 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
RIBOSOMAL PROTEIN L13 I 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
RIBOSOMAL PROTEIN L14 J 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
RIBOSOMAL PROTEIN L15 K 164 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
RIBOSOMAL PROTEIN L15E L 194 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
RIBOSOMAL PROTEIN L18 M 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
RIBOSOMAL PROTEIN L18E N 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
RIBOSOMAL PROTEIN L19E O 148 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
RIBOSOMAL PROTEIN L21E P 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
RIBOSOMAL PROTEIN L22 Q 154 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
RIBOSOMAL PROTEIN L23 R 84 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
RIBOSOMAL PROTEIN L24 S 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
RIBOSOMAL PROTEIN L24E T 66 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
RIBOSOMAL PROTEIN L29 U 70 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
RIBOSOMAL PROTEIN L30 V 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
RIBOSOMAL PROTEIN L31E W 91 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
RIBOSOMAL PROTEIN L32E X 240 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
RIBOSOMAL PROTEIN L37Ae Y 73 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
RIBOSOMAL PROTEIN L37E Z 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
RIBOSOMAL PROTEIN L39E 1 48 Haloarcula marismortui Mutation: ΔR31
Gene Name(s): rpl39e rrnAC3112
RIBOSOMAL PROTEIN L44E 2 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Macromolecule Entities
Molecule Chains Length Organism Details
23S RRNA 0 2922 Haloarcula marismortui
5S RRNA 9 122 Haloarcula marismortui

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CD
Query on CD

2, N, T, Y, Z CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

0 POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

0, 2, A, B, I, K, L, M, N, Q, X CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

0, 2, 9, A, B, J, S, X MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

0, 9, A, C, H, I, K, L, P, Q, R, S SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.189
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 211.66 α = 90.00
b = 299.67 β = 90.00
c = 573.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-07-03
  • Released Date: 2001-08-01
  • Deposition author(s): Klein, D.J., Schmeing, T.M., Moore, P.B., Steitz, T.A.

Revision History

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