8CQX | pdb_00008cqx

Ribokinase from T.sp mutant A92G

• PDB DOI: https://doi.org/10.2210/pdb8CQX/pdb

• Classification: HYDROLASE
• Organism(s): Thermus sp.
• Expression System: Thermus sp.
• Mutation(s): Yes 


• Deposited: 2023-03-07 Released: 2023-04-05 
• Deposition Author(s): Timofeev, V.I., Shevtsov, M.B., Abramchik, Y.A., Kostromina, M.A., Zayats, E.A., Kuranova, I.P., Esipov, R.S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Ribokinase from T.sp mutant A92G

Timofeev, V.I., Shevtsov, M.B., Abramchik, Y.A., Kostromina, M.A., Zayats, E.A., Kuranova, I.P., Esipov, R.S.

To be published.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 125.83 kDa 
• Atom Count: 9,056 
• Modeled Residue Count: 1,200 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D	300	Thermus sp.	Mutation(s): 1  Gene Names: rbsK
UniProt
Find proteins for A0ACD6B9W2 (Thermus sp. (strain 2.9)) Explore A0ACD6B9W2  Go to UniProtKB:  A0ACD6B9W2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	F [auth A], H [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.307	α = 90
b = 155.608	β = 96.37
c = 82.915	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Timofeev, V.I., Shevtsov, M.B., Abramchik, Y.A., Kostromina, M.A., Zayats, E.A., Kuranova, I.P., Esipov, R.S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection