5USE | pdb_00005use

5-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

• PDB DOI: https://doi.org/10.2210/pdb5USE/pdb
• NAKB: 5USE

• Classification: HYDROLASE / RNA / DNA
• Organism(s): synthetic construct, Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2017-02-13 Released: 2017-03-08 
• Deposition Author(s): Fang, Z., Qin, L., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.234 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate

Fang, Z., Dantsu, Y., Chen, C., Zhang, W., Huang, Z.

(2023) ChemistrySelect 8

• DOI: https://doi.org/10.1002/slct.202302253

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 20.16 kDa 
• Atom Count: 1,356 
• Modeled Residue Count: 144 
• Deposited Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease H	C [auth A]	142	Halalkalibacterium halodurans C-125	Mutation(s): 1  Gene Names: rnhA, BH0863 EC: 3.1.26.4
UniProt
Find proteins for Q9KEI9 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KEI9  Go to UniProtKB:  Q9KEI9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')	A [auth B]	6	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*(T5S)P*CP*G)-3')	B [auth C]	6	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth B], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.234 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.912	α = 90
b = 37.56	β = 96.17
c = 62.258	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Fang, Z., Qin, L., Huang, Z.

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2023-08-02
  Changes: Database references, Derived calculations
• Version 1.2: 2023-10-04
  Changes: Data collection, Refinement description