3Q9V | pdb_00003q9v

Crystal structure of rra c-terminal domain(123-221) from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb3Q9V/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-10 Released: 2012-01-11 
• Deposition Author(s): Liu, Y., Gao, Z.Q., Dong, Y.H., Ji, C.N.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of rra c-terminal domain (123-221) from Deinococcus radiodurans.

Liu, Y., Gao, Z.Q., Dong, Y.H., Ji, C.N.

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: 29.87 kDa 
• Atom Count: 1,794 
• Modeled Residue Count: 197 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	A, B	133	Deinococcus radiodurans	Mutation(s): 0  Gene Names: DR_2418
UniProt
Find proteins for Q9RRR8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RRR8  Go to UniProtKB:  Q9RRR8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.251	α = 90
b = 37.602	β = 113.92
c = 48.573	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Liu, Y., Gao, Z.Q., Dong, Y.H., Ji, C.N.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2009CB918600

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2022-02-23
  Changes: Database references, Derived calculations
• Version 1.3: 2022-07-27
  Changes: Advisory, Author supporting evidence, Data collection, Database references, Other, Refinement description, Source and taxonomy, Structure summary
• Version 2.0: 2022-08-03
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Other, Refinement description, Structure summary
• Version 2.1: 2022-08-17
  Changes: Database references
• Version 2.2: 2023-11-01
  Changes: Data collection, Refinement description