3Q20

Crystal structure of RbcX C103A mutant from Thermosynechococcus elongatus

• PDB DOI: https://doi.org/10.2210/pdb3Q20/pdb
• Entry: 3Q20 supersedes: 3KA1

• Classification: CHAPERONE
• Organism(s): Thermosynechococcus vestitus BP-1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-12-19 Released: 2011-01-26 
• Deposition Author(s): Tarnawski, M., Krzywda, S., Szczepaniak, A., Jaskolski, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.211 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Structure of the RuBisCO chaperone RbcX from the thermophilic cyanobacterium Thermosynechococcus elongatus

Tarnawski, M., Krzywda, S., Bialek, W., Jaskolski, M., Szczepaniak, A.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 851-857

• PubMed: 21821880 
• DOI: https://doi.org/10.1107/S1744309111018860
• Primary Citation of Related Structures:  
  3Q20


• PubMed Abstract: 
  

  The crystal structure of TeRbcX, a RuBisCO assembly chaperone from the cyanobacterium Thermosynechococcus elongatus, a thermophilic organism, has been determined at 1.7 Å resolution. TeRbcX has an unusual cysteine residue at position 103 that is not found in RbcX proteins from mesophilic organisms. Unlike wild-type TeRbcX, a mutant protein with Cys103 replaced by Ala (TeRbcX-C103A) could be readily crystallized. The structure revealed that the overall fold of the TeRbcX homodimer is similar to those of previously crystallized RbcX proteins. Normal-mode analysis suggested that TeRbcX might adopt an open or closed conformation through a hinge movement pivoted on a kink in two long α4 helices. This type of conformational transition is presumably connected to RbcL (the large RuBisCO subunit) binding during the chaperone function of the RuBisCO assembly.

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Organizational Affiliation: 

Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 29.5 kDa 
• Atom Count: 2,075 
• Modelled Residue Count: 220 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RbcX protein	A, B	126	Thermosynechococcus vestitus BP-1	Mutation(s): 1  Gene Names: rbcX, tll1505
UniProt
Find proteins for Q8DIS6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIS6  Go to UniProtKB:  Q8DIS6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	D [auth B], E [auth B]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
ACT	C [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.211 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.78	α = 90
b = 67.733	β = 90
c = 94.544	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Tarnawski, M., Krzywda, S., Szczepaniak, A., Jaskolski, M.
• This entry supersedes: 3KA1

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description