5TRD | pdb_00005trd

Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator

• PDB DOI: https://doi.org/10.2210/pdb5TRD/pdb
• NAKB: 5TRD

• Classification: TRANSFERASE/DNA
• Organism(s): Thermoplasma acidophilum DSM 1728, Thermoplasma acidophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-26 Released: 2016-11-23 
• Deposition Author(s): Vetting, M.W., Rodionova, I.A., Li, X., Osterman, A.L., Rodionov, D.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator

Vetting, M.W., Rodionova, I.A., Li, X., Osterman, A.L., Rodionov, D.A., Almo, S.C.

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)

Macromolecule Content 

• Total Structure Weight: 65.15 kDa 
• Atom Count: 4,721 
• Modeled Residue Count: 472 
• Deposited Residue Count: 498 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin kinase	A, B	230	Thermoplasma acidophilum DSM 1728	Mutation(s): 0  Gene Names: ribK, Ta1064 EC: 2.7.1.161
UniProt
Find proteins for Q9HJA6 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HJA6  Go to UniProtKB:  Q9HJA6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3')	C [auth G]	19	Thermoplasma acidophilum

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3')	D [auth H]	19	Thermoplasma acidophilum

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTP	E [auth A], G [auth B]	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N
NA	F [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.411	α = 90
b = 95.04	β = 113.51
c = 61.262	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Vetting, M.W., Rodionova, I.A., Li, X., Osterman, A.L., Rodionov, D.A., Almo, S.C.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description