5H7F | pdb_00005h7f

Crystal Structure of Mn-derivative drCPDase

• PDB DOI: https://doi.org/10.2210/pdb5H7F/pdb

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


• Deposited: 2016-11-18 Released: 2017-11-22 
• 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: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Mn-derivative drCPDase

Han, W., Hua, Y., Zhao, Y.

To be published.

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: 20.84 kDa 
• Atom Count: 1,542 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.2	α = 90
b = 91.2	β = 90
c = 170	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Han, W., Hua, Y., Zhao, Y.

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description