Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 20076.04 
• Atom Count: 1412 
• Residue Count: 147 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

6DOL

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 25 mM K+ for 120 s at 21 C (dataset 2)

• DOI: 10.2210/pdb6DOL/pdb
• Deposition Group: G_1001001 (undefined)

• Classification: HYDROLASE/DNA/RNA
• Organism(s): synthetic construct, Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2018-06-09 Released: 2018-08-15 
• Deposition Author(s): Samara, N.L., Yang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.433 Å
• R-Value Free: 0.185 
• R-Value Work: 0.151 

Literature

Cation trafficking propels RNA hydrolysis.

Samara, N.L., Yang, W.

(2018) Nat. Struct. Mol. Biol. 25: 715-721

• PubMed: 30076410 
• Primary Citation of Related Structures:  
  6DP8, 6DP6, 6DP5, 6DP4, 6DP3, 6DP2, 6DP1, 6DP0, 6DOZ, 6DOY, 6DOI, 6DPP, 6DPO, 6DPN, 6DPM, 6DPK, 6DPL, 6DPJ, 6DPI, 6DPH, 6DPG, 6DPF, 6DPE, 6DPD, 6DPC, 6DPB, 6DPA, 6DP9, 6DP7, 6DOX, 6DOV, 6DOW, 6DOU, 6DOT, 6DOS, 6DOR, 6DOP, 6DOQ, 6DOO, 6DON,
  6DP8, 6DP6, 6DP5, 6DP4, 6DP3, 6DP2, 6DP1, 6DP0, 6DOZ, 6DOY, 6DOI, 6DPP, 6DPO, 6DPN, 6DPM, 6DPK, 6DPL, 6DPJ, 6DPI, 6DPH, 6DPG, 6DPF, 6DPE, 6DPD, 6DPC, 6DPB, 6DPA, 6DP9, 6DP7, 6DOX, 6DOV, 6DOW, 6DOU, 6DOT, 6DOS, 6DOR, 6DOP, 6DOQ, 6DOO, 6DON, 6DOM, 6DOK, 6DOJ, 6DOH, 6DOG, 6DOF, 6DOE, 6DOD, 6DOC, 6DOB, 6DOA, 6DO9, 6DO8, 6DMV, 6DMN

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ribonuclease H	A	135	Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)	Mutation(s): 0  Gene Names: rnhA EC: 3.1.26.4
Find proteins for Q9KEI9 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Go to UniProtKB:  Q9KEI9

Entity ID: 2
Molecule	Chains	Length	Organism
5'-R(*AP*CP*AP*U)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')	B	4	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism
5'-R(P*CP*G)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')	b	2	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism
DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')	C	6	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	A, C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.433 Å
• R-Value Free: 0.185 
• R-Value Work: 0.151 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 81.801	α = 90.00
b = 37.113	β = 96.44
c = 62.105	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
Aimless	data scaling
PHENIX	phasing
HKL-2000	data reduction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-06-09 
• Released Date: 2018-08-15 
• Deposition Author(s): Samara, N.L., Yang, W.

Revision History 

• Version 1.0: 2018-08-15
  Type: Initial release