3WR2 | pdb_00003wr2

RNase Po1 complexed with 3'GMP

• PDB DOI: https://doi.org/10.2210/pdb3WR2/pdb

• Classification: HYDROLASE
• Organism(s): Pleurotus ostreatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-13 Released: 2015-02-18 
• Deposition Author(s): Hara, Y., Katsutani, T., Kobayashi, H., Suzuki, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

RNase Po1 complexed with 3'GMP

Hara, Y., Katsutani, T., Kobayashi, H., 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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.55 kDa 
• Atom Count: 5,390 
• Modeled Residue Count: 606 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanyl-specific ribonuclease Po1	A, B, C, D, E, F	101	Pleurotus ostreatus	Mutation(s): 0  EC: 4.6.1.24
UniProt
Find proteins for P81762 (Pleurotus ostreatus) Explore P81762  Go to UniProtKB:  P81762

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3GP (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	GUANOSINE-3'-MONOPHOSPHATE C10 H14 N5 O8 P ZDPUTNZENXVHJC-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.072	α = 90
b = 95.866	β = 90
c = 106.225	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Hara, Y., Katsutani, T., Kobayashi, H., Suzuki, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 2.0: 2022-07-20
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2022-10-12
  Changes: Other
• Version 2.2: 2023-11-08
  Changes: Data collection, Refinement description
• Version 2.3: 2024-10-09
  Changes: Structure summary