5GY6 | pdb_00005gy6

Ribonuclease from Hericium erinaceus (RNase He1)

• PDB DOI: https://doi.org/10.2210/pdb5GY6/pdb

• Classification: HYDROLASE
• Organism(s): Hericium erinaceus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-21 Released: 2017-09-27 
• Deposition Author(s): Kobayashi, H., Sangawa, T., Takebe, K., Itagaki, T., Motoyoshi, N., Suzuki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Ribonuclease from Hericium erinaceus (RNase He1)

Kobayashi, H., Sangawa, T., Takebe, K., Itagaki, T., Motoyoshi, N., Suzuki, M.

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: 10.78 kDa 
• Atom Count: 824 
• Modeled Residue Count: 88 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease T1	A	100	Hericium erinaceus	Mutation(s): 0  Gene Names: RNHe1 EC: 3.1.27.3
UniProt
Find proteins for B1Q4V2 (Hericium erinaceus) Explore B1Q4V2  Go to UniProtKB:  B1Q4V2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.701	α = 90
b = 42.945	β = 90
c = 60.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Kobayashi, H., Sangawa, T., Takebe, K., Itagaki, T., Motoyoshi, N., Suzuki, M.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary