4ZBP

Crystal structure of the AMPCPR-bound AtNUDT7

• PDB DOI: https://doi.org/10.2210/pdb4ZBP/pdb

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


• Deposited: 2015-04-15 Released: 2015-09-09 
• Deposition Author(s): Tang, Q., Liu, C., Zhong, C., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

Crystal Structures of Arabidopsis thaliana Nudix Hydrolase NUDT7 Reveal a Previously Unobserved Conformation.

Tang, Q., Liu, C., Zhong, C., Ding, J.

(2015) Mol Plant 8: 1557-1559

• PubMed: 26253775 
• DOI: https://doi.org/10.1016/j.molp.2015.07.010
• Primary Citation of Related Structures:  
  4ZB3, 4ZBP

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Organizational Affiliation: 

National Center for Protein Sciences Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

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 2  

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

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

Macromolecule Content

• Total Structure Weight: 106.52 kDa 
• Atom Count: 6,428 
• Modelled Residue Count: 790 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase 7	A, B, C	310	Arabidopsis thaliana	Mutation(s): 0  Gene Names: NUDT7, GFG1, NUDX7, At4g12720, T20K18.70 EC: 3.6.1 (PDB Primary Data), 3.6.1.13 (PDB Primary Data), 3.6.1.22 (PDB Primary Data)
UniProt
Find proteins for Q9SU14 (Arabidopsis thaliana) Explore Q9SU14  Go to UniProtKB:  Q9SU14

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADV	G [auth C]	ALPHA-BETA METHYLENE ADP-RIBOSE C16 H25 N5 O13 P2 ZPZRETFSCSWNDT-DBXCYWGHSA-N
SO4	D [auth A], E [auth B], F [auth B], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.202	α = 90
b = 258.72	β = 90
c = 157.548	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Tang, Q., Liu, C., Zhong, C., Ding, J.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description