4LQ4 | pdb_00004lq4

crystal structure of mutant ribosomal protein L1 from Methanococcus jannaschii with deletion of 8 residues from C-terminus

• PDB DOI: https://doi.org/10.2210/pdb4LQ4/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-17 Released: 2014-07-02 
• Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, S.V., Shkliaeva, A.A., Garber, M.B., Nikonov, S.V., Sarskikh, A.V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a mutant of archaeal ribosomal protein L1 from Methanococcus jannaschii

Sarskikh, A.V., Gabdulkhakov, A.G., Kostareva, O.S., Shkliaeva, A.A., Tishchenko, S.V.

(2014) Crystallogr Rep 59: 394-398

• DOI: https://doi.org/10.1134/S1063774514030158

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: 24.18 kDa 
• Atom Count: 1,914 
• Modeled Residue Count: 211 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	A	211	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: MJ0510, rpl1, rplA
UniProt
Find proteins for P54050 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore P54050  Go to UniProtKB:  P54050

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
IPA	C [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.868	α = 90
b = 105.255	β = 104.01
c = 38.526	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, S.V., Shkliaeva, A.A., Garber, M.B., Nikonov, S.V., Sarskikh, A.V.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description