4NYN | pdb_00004nyn

Crystal structure of RNase H1 from halophilic archaeon Halobacterium salinarum NRC-1

• PDB DOI: https://doi.org/10.2210/pdb4NYN/pdb

• Classification: HYDROLASE
• Organism(s): Halobacterium salinarum NRC-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-11 Released: 2014-02-12 
• Deposition Author(s): You, D.J., Angkawidjaja, C., Koga, Y., Kanaya, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RNase H1 from halophilic archaeon Halobacterium salinarum NRC-1

You, D.J., Angkawidjaja, C., Koga, Y., Kanaya, S.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.28 kDa 
• Atom Count: 2,300 
• Modeled Residue Count: 265 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease HI	A, B	199	Halobacterium salinarum NRC-1	Mutation(s): 0  Gene Names: rnhA, VNG_0255C EC: 3.1.26.4
UniProt
Find proteins for Q9HSF6 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore Q9HSF6  Go to UniProtKB:  Q9HSF6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.802	α = 90
b = 115.802	β = 90
c = 38.282	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): You, D.J., Angkawidjaja, C., Koga, Y., Kanaya, S.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description