7YKM | pdb_00007ykm

Structure of DciA DUF721 domain from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb7YKM/pdb

• Classification: REPLICATION
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-22 Released: 2023-08-02 
• Deposition Author(s): Cheng, K.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Structure of DciA DUF721 domain from Deinococcus radiodurans

Cheng, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 11.65 kDa 
• Atom Count: 689 
• Modeled Residue Count: 81 
• Deposited Residue Count: 105 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DciA DUF721 domain	A	105	Deinococcus radiodurans	Mutation(s): 0  Gene Names: DR_1088
UniProt
Find proteins for Q9RVE1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RVE1  Go to UniProtKB:  Q9RVE1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.593	α = 90
b = 37.438	β = 164.339
c = 86.285	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Cheng, K.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100017

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection