5CDL | pdb_00005cdl

Proline dipeptidase from Deinococcus radiodurans (selenomethionine derivative)

• PDB DOI: https://doi.org/10.2210/pdb5CDL/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-07-04 Released: 2016-08-10 
• Deposition Author(s): Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Proline dipeptidase from Deinococcus radiodurans (selenomethionine derivative)

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

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: 37.77 kDa 
• Atom Count: 2,922 
• Modeled Residue Count: 349 
• 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): 1  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	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.632	α = 90
b = 60.632	β = 90
c = 202.824	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
Coot	model building
RESOLVE	phasing
SOLVE	phasing
Aimless	data scaling
XDS	data processing
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2018-07-04
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary