6ZNX | pdb_00006znx

Ribokinase from Thermus Species

• PDB DOI: https://doi.org/10.2210/pdb6ZNX/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus sp. 2.9
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-07 Released: 2020-07-15 
• Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Tuzova, E.S., Esipova, L.V., Mikheeva, O.O., Kostromina, M.A., Kuranova, I.P., Esipov, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Ribokinase from Thermus Species

Timofeev, V.I., Abramchik, Y.A., Tuzova, E.S., Esipova, L.V., Mikheeva, O.O., Kostromina, M.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: 125.81 kDa 
• Atom Count: 8,553 
• Modeled Residue Count: 1,138 
• 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. 2.9	Mutation(s): 0  Gene Names: rbsK, QT17_05185 EC: 2.7.1.15

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], F [auth B], G [auth C], H [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.21	α = 90
b = 155.55	β = 98.2
c = 83.04	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Tuzova, E.S., Esipova, L.V., Mikheeva, O.O., Kostromina, M.A., Kuranova, I.P., Esipov, R.S.

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description