1DWU | pdb_00001dwu

Ribosomal protein L1

• PDB DOI: https://doi.org/10.2210/pdb1DWU/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Methanothermococcus thermolithotrophicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-12-13 Released: 2000-12-07 
• Deposition Author(s): Tishchenko, S.V., Nevskaya, N.A., Pavelyev, M.N., Nikonov, S.V., Garber, M.B., Piendl, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.305 (Depositor) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of Ribosomal Protein L1 from Methanococcus Thermolithotrophicus. Functionally Important Structural Invariants on the L1 Surface

Nevskaya, N.A., Tishchenko, S.V., Paveliev, M., Smolinskaya, Y., Fedorov, R., Piendl, W., Nakamura, Y., Toyoda, T., Garber, M.B., Nikonov, S.V.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1023

• PubMed: 12037305 
• DOI: https://doi.org/10.1107/s0907444902006157
• Primary Citation Related Structures: 
  1DWU


• PubMed Abstract: 
  

  The crystal structure of ribosomal protein L1 from the archaeon Methanococcus thermolithotrophicus has been determined at 2.7 A resolution. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 67.0, b = 70.1, c = 106.3 A and two molecules per asymmetric unit. The structure was solved by the molecular-replacement method with AMoRe and refined with CNS to an R value of 18.9% and an R(free) of 25.4% in the resolution range 30-2.7 A. Comparison of this structure with those obtained previously for two L1 proteins from other sources (the bacterium Thermus thermophilus and the archaeon M. jannaschii) as well as detailed analysis of intermolecular contacts in the corresponding L1 crystals reveal structural invariants on the molecular surface which are probably important for binding the 23S ribosomal RNA and protein function within the ribosome.

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Organizational Affiliation: 
• Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 47.66 kDa 
• Atom Count: 3,336 
• Modeled Residue Count: 426 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L1	A, B	213	Methanothermococcus thermolithotrophicus	Mutation(s): 0  Gene Names: THE CORRESPONDING GENE IN E. COLI IS RPLA
UniProt
Find proteins for O52704 (Methanothermococcus thermolithotrophicus) Explore O52704  Go to UniProtKB:  O52704

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.305 (Depositor) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.36	α = 90
b = 69.98	β = 90
c = 106.17	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-07 
Deposition Author(s): Tishchenko, S.V., Nevskaya, N.A., Pavelyev, M.N., Nikonov, S.V., Garber, M.B., Piendl, W.

Revision History  

• Version 1.0: 2000-12-07
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2023-12-06
  Changes: Data collection, Database references, Other, Refinement description