3UMY

Crystal structure of mutant ribosomal protein T217A TthL1 in complex with 80nt 23S RNA from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb3UMY/pdb
• NAKB: 3UMY

• Classification: rRNA BINDING protein/RNA
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-11-15 Released: 2012-10-31 
• Deposition Author(s): Gabdulkhakov, A.G., Nevskaya, N.A., Nikonov, S.V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Crystal structure of mutant ribosomal protein T217A TthL1 in complex with 80nt 23S RNA from Thermus thermophilus

Tishchenko, S.V., Nikonova, E.Y., Kostareva, O.S., Gabdulkhakov, A.G., Sarskikh, A.V., Piendl, W., Nikonov, S.V., Garber, M.B., Nevskaya, N.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.35 kDa 
• Atom Count: 3,689 
• Modelled Residue Count: 308 
• Deposited Residue Count: 308 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	A	228	Thermus thermophilus	Mutation(s): 1  Gene Names: rplA, rpl1
UniProt
Find proteins for P27150 (Thermus thermophilus) Explore P27150  Go to UniProtKB:  P27150

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (80-MER)	B	80	Thermus thermophilus

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth B], H [auth B], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.11	α = 90
b = 68.82	β = 90
c = 88.83	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Gabdulkhakov, A.G., Nevskaya, N.A., Nikonov, S.V.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description