4KVB

Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17

Structural Biology Knowledgebase: 4KVB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.217

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KVB

Classification: RIBOSOME

Total Structure Weight: 776899.75


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TT_C0509
30S ribosomal protein S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TT_C1322
30S ribosomal protein S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TT_C1301
30S ribosomal protein S5 E 162 Thermus thermophilus Gene Name(s): rpsE rps5 TT_C1311
30S ribosomal protein S6 F 101 Thermus thermophilus Gene Name(s): rpsF rps6 TT_C1740
30S ribosomal protein S7 G 156 Thermus thermophilus Gene Name(s): rpsG rps7 TT_C1332
30S ribosomal protein S8 H 138 Thermus thermophilus Gene Name(s): rpsH rps8 TT_C1314
30S ribosomal protein S9 I 128 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
30S ribosomal protein S10 J 105 Thermus thermophilus Gene Name(s): rpsJ rps10 TT_C1329
30S ribosomal protein S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TT_C1302
30S ribosomal protein S12 L 134 Thermus thermophilus Gene Name(s): rpsL rps12 TT_C1333
30S ribosomal protein S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TT_C1303
30S ribosomal protein S14 type Z N 61 Thermus thermophilus Gene Name(s): rpsZ rps14 rpsN TT_C1315
30S ribosomal protein S15 O 89 Thermus thermophilus Gene Name(s): rpsO rps15 TT_C0773
30S ribosomal protein S16 P 88 Thermus thermophilus Gene Name(s): rpsP rps16 TT_C0673
30S ribosomal protein S18 R 88 Thermus thermophilus Gene Name(s): rpsR rps18 TT_C1742
30S ribosomal protein S19 S 93 Thermus thermophilus Gene Name(s): rpsS rps19 TT_C1324
30S ribosomal protein S20 T 106 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
30S ribosomal protein Thx U 27 Thermus thermophilus Gene Name(s): rpsU TT_C1030
Macromolecule Entities
Molecule Chains Length Organism Details
16S rRNA A 1522 Thermus thermophilus

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

D, N ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

A, B, D, E, M, U MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 9 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
A RNA LINKING C9 H13 N2 O9 P U
7MG
Query on 7MG
A RNA LINKING C11 H18 N5 O8 P G
M2G
Query on M2G
A RNA LINKING C12 H18 N5 O8 P G
5MC
Query on 5MC
A RNA LINKING C10 H16 N3 O8 P C
2MG
Query on 2MG
A RNA LINKING C11 H16 N5 O8 P G
4OC
Query on 4OC
A RNA LINKING C11 H18 N3 O8 P C
UR3
Query on UR3
A RNA LINKING C10 H15 N2 O9 P U
MA6
Query on MA6
A RNA LINKING C12 H18 N5 O7 P A
0TD
Query on 0TD
L L-PEPTIDE LINKING C5 H9 N O4 S ASP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.2 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.217
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 397.32 α = 90.00
b = 397.32 β = 90.00
c = 215.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-22
  • Released Date: 2014-06-04
  • Deposition author(s): Murphy, E.L., Jogl, G.

Revision History

No revisions since initial release