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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.299 (Depositor), 0.295 (DCC)
R-Value Work:
0.247 (Depositor), 0.251 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of PprA filament from Deinococcus peraridilitoris

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L0A1P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.295 (DCC)
R-Value Work: 0.247 (Depositor), 0.251 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.