2R7Y

Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N

• PDB DOI: https://doi.org/10.2210/pdb2R7Y/pdb
• NAKB: 2R7Y

• Classification: Hydrolase/RNA/DNA
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-09-10 Released: 2008-05-06 
• Deposition Author(s): Jiang, J.-S., Gerlits, O., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N

Jiang, J.-S., Gerlits, O., Huang, Z.

To be published.

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: 19.21 kDa 
• Atom Count: 1,506 
• Modelled Residue Count: 144 
• Deposited Residue Count: 144 
• 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]	132	Halalkalibacterium halodurans	Mutation(s): 1  Gene Names: rnhA 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	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DAP*DTP*(SDG)P*DTP*DCP*(SDG))-3')	B [auth C]	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.66	α = 90
b = 37.819	β = 96.6
c = 61.937	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Jiang, J.-S., Gerlits, O., Huang, Z.

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection