5GIU

Crystal structure of Xaa-Pro peptidase from Deinococcus radiodurans, metal-free active site

• PDB DOI: https://doi.org/10.2210/pdb5GIU/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-25 Released: 2017-06-28 
• Deposition Author(s): Are, V.N., Kumar, A., Singh, R., Ghosh, B., Jamdar, S.N., Makde, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.200 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Xaa-Pro peptidase from Deinococcus radiodurans, metal-free active site

Are, V.N., Kumar, A., Singh, R., Ghosh, B., Jamdar, S.N., Makde, R.D.

To be published.

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: 37.31 kDa 
• Atom Count: 2,793 
• Modelled Residue Count: 347 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline dipeptidase	A	349	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_1246
UniProt
Find proteins for Q9RUY4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RUY4  Go to UniProtKB:  Q9RUY4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.200 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.327	α = 90
b = 60.327	β = 90
c = 203.515	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
Aimless	data scaling
XDS	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Are, V.N., Kumar, A., Singh, R., Ghosh, B., Jamdar, S.N., Makde, R.D.

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description