1AD2 | pdb_00001ad2

RIBOSOMAL PROTEIN L1 MUTANT WITH SERINE 179 REPLACED BY CYSTEINE

• PDB DOI: https://doi.org/10.2210/pdb1AD2/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 1997-02-20 Released: 1997-05-15 
• Deposition Author(s): Unge, J., Al-Karadaghi, S., Liljas, A., Jonsson, B.-H., Eliseikina, I., Ossina, N., Nevskaya, N., Fomenkova, N., Garber, M., Nikonov, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.270 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

A mutant form of the ribosomal protein L1 reveals conformational flexibility.

Unge, J., Al-Karadaghi, S., Liljas, A., Jonsson, B.H., Eliseikina, I., Ossina, N., Nevskaya, N., Fomenkova, N., Garber, M., Nikonov, S.

(1997) FEBS Lett 411: 53-59

• PubMed: 9247141 
• DOI: https://doi.org/10.1016/s0014-5793(97)00611-x
• Primary Citation Related Structures: 
  1AD2


• PubMed Abstract: 
  

  The crystal structure of the mutant S179C of the ribosomal protein L1 from Thermus thermophilus has been determined at 1.9 A resolution. The mutant molecule displays a small but significant opening of the cavity between the two domains. The domain movement seems to be facilitated by the flexibility of at least two conserved glycines. These glycines may be necessary for the larger conformational change needed for an induced fit mechanism upon binding RNA. The domain movement makes a disulfide bridge possible between the incorporated cysteines in two monomers of the mutant L1.

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Organizational Affiliation: 
• Department of Molecular Biophysics, University of Lund, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.36 kDa 
• Atom Count: 1,858 
• Modeled Residue Count: 224 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L1	A	228	Thermus thermophilus	Mutation(s): 1
UniProt
Find proteins for P27150 (Thermus thermophilus) Explore P27150  Go to UniProtKB:  P27150

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	E [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
MRD	F [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.270 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.1	α = 90
b = 61.4	β = 90
c = 46.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-05-15 
Deposition Author(s): Unge, J., Al-Karadaghi, S., Liljas, A., Jonsson, B.-H., Eliseikina, I., Ossina, N., Nevskaya, N., Fomenkova, N., Garber, M., Nikonov, S.

Revision History  

• Version 1.0: 1997-05-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-02-07
  Changes: Data collection
• Version 1.5: 2026-03-04
  Changes: Refinement description, Structure summary