7W05

12 mutant Ribonuclease from Hericium erinaceus GMP binding form

• PDB DOI: https://doi.org/10.2210/pdb7W05/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Hericium erinaceus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-11-17 Released: 2022-11-23 
• Deposition Author(s): Takebe, K., Chida, T., Suzuki, M., Itagaki, T., Morita, Y., Uzawa, N., Kobayashi, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.166 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Starting Model: experimental

Literature

12 mutant Ribonuclease from Hericium erinaceus GMP binding form

Takebe, K., Chida, T., Suzuki, M., Uzawa, N., 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)

Macromolecule Content

• Total Structure Weight: 11.09 kDa 
• Atom Count: 930 
• Modelled Residue Count: 100 
• 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): 12  Gene Names: RNHe1
UniProt
Find proteins for B1Q4V2 (Hericium erinaceus) Explore B1Q4V2  Go to UniProtKB:  B1Q4V2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.166 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.589	α = 90
b = 46.31	β = 90
c = 53.524	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Takebe, K., Chida, T., Suzuki, M., Itagaki, T., Morita, Y., Uzawa, N., Kobayashi, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20K21676

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary