7DOX | pdb_00007dox

The structure of the Arabidopsis thaliana guanosine deaminase in complex with m7G

• PDB DOI: https://doi.org/10.2210/pdb7DOX/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-12-17 Released: 2022-02-02 
• Deposition Author(s): Xie, W., Jia, Q., Zeng, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Asymmetric Catalysis of Arabidopsis thaliana Guanosine Deaminase Revealed by Crystal Structures

Xie, W., Jia, Q., Zeng, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 35.77 kDa 
• Atom Count: 2,713 
• Modeled Residue Count: 314 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanosine deaminase	A, B [auth D]	161	Arabidopsis thaliana	Mutation(s): 0  Gene Names: GSDA, TAD4, At5g28050 EC: 3.5.4.15
UniProt
Find proteins for Q94BU8 (Arabidopsis thaliana) Explore Q94BU8  Go to UniProtKB:  Q94BU8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG7 (Subject of Investigation/LOI)	D [auth A], F [auth D]	7-METHYLGUANOSINE C11 H16 N5 O5 OGHAROSJZRTIOK-KQYNXXCUSA-O
ZN (Subject of Investigation/LOI)	C [auth A], E [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.136	α = 90
b = 119.136	β = 90
c = 39.812	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Xie, W., Jia, Q., Zeng, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870782

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description