3CC2

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

Structural Biology Knowledgebase: 3CC2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3CC2

Classification: RIBOSOME

Total Structure Weight: 1484619.50


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2P A 240 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
50S ribosomal protein L3P B 338 Haloarcula marismortui Gene Name(s): rpl3 rrnAC1611
50S ribosomal protein L4P C 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
50S ribosomal protein L5P D 177 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
50S ribosomal protein L6P E 178 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
50S ribosomal protein L7Ae F 120 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
50S ribosomal protein L10E G 348 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
50S ribosomal protein L10e H 177 Haloarcula marismortui Gene Name(s): rpl10e rrnAC2357
50S ribosomal protein L11P I 162 Haloarcula marismortui Gene Name(s): rpl11 rrnAC1414
50S ribosomal protein L13P J 145 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
50S ribosomal protein L14P K 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
50S ribosomal protein L15P L 165 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
50S ribosomal protein L15e M 196 Haloarcula marismortui Gene Name(s): rpl15e rrnAC2065
50S ribosomal protein L18P N 187 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
50S ribosomal protein L18e O 116 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
50S ribosomal protein L19e P 149 Haloarcula marismortui Gene Name(s): rpl19e rrnAC1594
50S ribosomal protein L21e Q 96 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
50S ribosomal protein L22P R 155 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
50S ribosomal protein L23P S 85 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
50S ribosomal protein L24P T 120 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
50S ribosomal protein L24e U 67 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
50S ribosomal protein L29P V 71 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
50S ribosomal protein L30P W 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
50S ribosomal protein L31e X 92 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
50S ribosomal protein L32e Y 241 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
50S ribosomal protein L37Ae Z 116 Haloarcula marismortui Gene Name(s): rpl37ae rrnAC1669
50S ribosomal protein L37e 1 57 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
50S ribosomal protein L39e 2 50 Haloarcula marismortui Gene Name(s): rpl39e rrnAC3112
50S ribosomal protein L44E 3 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Macromolecule Entities
Molecule Chains Length Organism Details
23S RIBOSOMAL RNA 0 2923 Haloarcula marismortui
5S RIBOSOMAL RNA 9 122 Haloarcula marismortui

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

1, 3, O, U, 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, 3, A, B, J, L, M, N, O, R, Y CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

0, 3, 9, A, B, K, T, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

0, 9, A, C, H, J, L, M, Q, R, S SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 5 Unique
ID Chains Type Formula 2D Diagram Parent
1MA
Query on 1MA
0 RNA LINKING C11 H16 N5 O7 P A
OMU
Query on OMU
0 RNA LINKING C10 H15 N2 O9 P U
OMG
Query on OMG
0 RNA LINKING C11 H16 N5 O8 P G
UR3
Query on UR3
0 RNA LINKING C10 H15 N2 O9 P U
PSU
Query on PSU
0 RNA LINKING C9 H13 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.199
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 211.65 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: 2008-02-23
  • Released Date: 2008-05-20
  • Deposition author(s): Gurel, G., Blaha, G.

Revision History

  • 2014-05-14
    Type: Other | Details: Update cell angles
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update