4ZB3 | pdb_00004zb3

Crystal structure of the apo AtNUDT7

• PDB DOI: https://doi.org/10.2210/pdb4ZB3/pdb

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


• Deposited: 2015-04-14 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: 2.30 Å
• R-Value Free: 
  0.226 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

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 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.
State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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; School of Life Science and Technology, Shanghai Tech University, 319 Yue-Yang Road, Shanghai 200031, China. Electronic address: [e-mail].

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)

Macromolecule Content 

• Total Structure Weight: 35.29 kDa 
• Atom Count: 2,197 
• Modeled Residue Count: 262 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase 7	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.226 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.788	α = 90
b = 116.788	β = 90
c = 115.735	γ = 120

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: 2024-03-20
  Changes: Data collection, Database references, Derived calculations