6LS1 | pdb_00006ls1

Ribonuclease from Hericium erinaceus active and GMP binding form

• PDB DOI: https://doi.org/10.2210/pdb6LS1/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Hericium erinaceus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-16 Released: 2021-01-20 
• Deposition Author(s): Takebe, K., Suzuki, M., Sangawa, T., Kobayashi, H., Itagaki, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Ribonuclease from Hericium erinaceus active and GMP binding form

Takebe, K., Suzuki, M., Sangawa, T., Kobayashi, H.

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: 21.92 kDa 
• Atom Count: 1,756 
• Modeled Residue Count: 200 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GMP (Subject of Investigation/LOI)	C [auth A]	GUANOSINE C10 H13 N5 O5 NYHBQMYGNKIUIF-UUOKFMHZSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.76	α = 90
b = 97.76	β = 90
c = 68.91	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Takebe, K., Suzuki, M., Sangawa, T., Kobayashi, H., Itagaki, T.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary