6O5L | pdb_00006o5l

Crystal structure of PprA filament from Deinococcus peraridilitoris

• PDB DOI: https://doi.org/10.2210/pdb6O5L/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Deinococcus peraridilitoris DSM 19664
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-03-04 Released: 2019-03-13 
• Deposition Author(s): Szabla, R., Junop, M.S., Rok, M.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PprA filament from Deinococcus peraridilitoris

Szabla, R., Czerwinski, M., Junop, M.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 34.71 kDa 
• Atom Count: 1,992 
• Modeled Residue Count: 271 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PprA	A	306	Deinococcus peraridilitoris DSM 19664	Mutation(s): 2  Gene Names: Deipe_2275
UniProt
Find proteins for L0A1P5 (Deinococcus peraridilitoris (strain DSM 19664 / LMG 22246 / CIP 109416 / KR-200)) Explore L0A1P5  Go to UniProtKB:  L0A1P5

Small Molecules

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: 3.30 Å
• R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.468	α = 90
b = 79.468	β = 90
c = 262.804	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
PHASER	phasing
PHENIX	refinement
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Szabla, R., Junop, M.S., Rok, M.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	2008R00075

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary