5H7E

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.196
R-Value Work: 0.175
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X17004964
Primary Citation of 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.

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.

Macromolecule Content

Total Structure Weight: 21.12 kDa
Atom Count: 1,560
Modelled Residue Count: 182
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for O32509 (Deinococcus radiodurans) Explore O32509 Go to UniProtKB: O32509
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32509
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]