3QOY | pdb_00003qoy

Crystal structure of ribosomal protein L1 from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb3QOY/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-11 Released: 2011-12-28 
• Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, S.V., Nikonova, E.U., Shkliaeva, A.A., Garber, M.B., Nikonov, S.V., Nevskaya, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.251 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Ribosomal Protein L1 from the Bacterium Aquifex Aeolicus

Nikonova, E.Yu., Tishchenko, S.V., Gabdulkhakov, A.G., Shklyaeva, A.A., Garber, M.B., Nikonov, S.V., Nevskaya, N.A.

(2011) Crystallogr Rep 56: 603-607

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: 27.33 kDa 
• Atom Count: 2,005 
• Modeled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	A	242	Aquifex aeolicus	Mutation(s): 0  Gene Names: aq_1935, rplA
UniProt
Find proteins for O67759 (Aquifex aeolicus (strain VF5)) Explore O67759  Go to UniProtKB:  O67759

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.251 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.49	α = 90
b = 37.52	β = 110.32
c = 58.97	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: 2011-12-28 
Deposition Author(s): Gabdulkhakov, A.G., Tishchenko, S.V., Nikonova, E.U., Shkliaeva, A.A., Garber, M.B., Nikonov, S.V., Nevskaya, N.A.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description