7DLC | pdb_00007dlc

The structure of the Arabidopsis thaliana guanosine deaminase in reaction with N1-methylguanosine

• PDB DOI: https://doi.org/10.2210/pdb7DLC/pdb

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


• Deposited: 2020-11-27 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: 2.45 Å
• R-Value Free: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (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: 2,503 
• 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
H93 (Subject of Investigation/LOI)	D [auth A], F [auth D]	2-azanyl-9-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-purin-6-one C11 H15 N5 O5 UTAIYTHAJQNQDW-KQYNXXCUSA-N
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: 2.45 Å
• R-Value Free:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.102	α = 90
b = 120.102	β = 90
c = 40.087	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