3ULD | pdb_00003uld

High resolution structure of DNA/RNA hybrid in complex with RNase H catalytic domain D132N mutant

• PDB DOI: https://doi.org/10.2210/pdb3ULD/pdb
• NAKB: 3ULD

• Classification: HYDROLASE/RNA/DNA
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2011-11-10 Released: 2012-11-14 
• Deposition Author(s): Gan, J.H., Abdur, R., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

RNA/DNA hybrid in complex with RNase H catalytic domain mutant D132N

Gan, J.H., Abdur, R., 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: 20.21 kDa 
• Atom Count: 1,480 
• Modeled Residue Count: 145 
• Deposited Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease H	A	142	Halalkalibacterium halodurans	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: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3')	B	6	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*TP*CP*(PGN))-3')	C	6	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.301	α = 90
b = 37.672	β = 96.76
c = 62.378	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Gan, J.H., Abdur, R., Huang, Z.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description