3W52 | pdb_00003w52

Zinc-dependent bifunctional nuclease

• PDB DOI: https://doi.org/10.2210/pdb3W52/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Agrobacterium tumefaciens
• Mutation(s): No 


• Deposited: 2013-01-18 Released: 2013-04-17 
• Deposition Author(s): Chou, T.L., Ko, T.P., Ko, C.Y., Shaw, J.F., Wang, A.H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Mechanistic insights to catalysis by a zinc-dependent bi-functional nuclease from Arabidopsis thaliana

Chou, T.L., Ko, T.P., Ko, C.Y., Lin, T.Y., Guo, R.T., Yu, T.F., Chan, H.C., Shaw, J.F., Wang, A.H.J.

(2013) Biocatal Agric Biotechnol 

• DOI: https://doi.org/10.1016/j.bcab.2013.03.006

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 32.66 kDa 
• Atom Count: 2,549 
• Modeled Residue Count: 256 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease 2	A	269	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ENDO2, At1g68290, T22E19.8 EC: 3.1.30.1
UniProt
Find proteins for Q9C9G4 (Arabidopsis thaliana) Explore Q9C9G4  Go to UniProtKB:  Q9C9G4
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	E [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
SO4	I [auth A], J [auth A], K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.254	α = 90
b = 66.727	β = 90
c = 99.487	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Chou, T.L., Ko, T.P., Ko, C.Y., Shaw, J.F., Wang, A.H.J.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary