5H7E | pdb_00005h7e

Crystal Structure of native drCPDase

• PDB DOI: https://doi.org/10.2210/pdb5H7E/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-11-18 Released: 2017-09-27 
• Deposition Author(s): Han, W., Hua, Y., Zhao, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the RNA 2',3'-cyclic phosphodiesterase from Deinococcus radiodurans

Han, W., Cheng, J., Zhou, C., Hua, Y., Zhao, Y.

(2017) Acta Crystallogr F Struct Biol Commun 73: 276-280

• PubMed: 28471359 
• DOI: https://doi.org/10.1107/S2053230X17004964
• Primary Citation Related Structures: 
  5H7E


• PubMed Abstract: 
  

  2',3'-Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase from Deinococcus radiodurans was crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism.

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Organizational Affiliation: 
• Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Sciences, Zhejiang University, People's Republic of China.

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: 21.12 kDa 
• Atom Count: 1,560 
• Modeled Residue Count: 182 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA 2',3'-cyclic phosphodiesterase	A	182	Deinococcus radiodurans	Mutation(s): 0  Gene Names: DR_2339 EC: 3.1.4 (PDB Primary Data), 3.1.4.58 (UniProt)
UniProt
Find proteins for O32509 (Deinococcus radiodurans) Explore O32509  Go to UniProtKB:  O32509

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.22	α = 90
b = 91.22	β = 90
c = 169.83	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Han, W., Hua, Y., Zhao, Y.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description