3AUY | pdb_00003auy

Crystal structure of Rad50 bound to ADP

• PDB DOI: https://doi.org/10.2210/pdb3AUY/pdb

• Classification: RECOMBINATION
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-18 Released: 2011-05-25 
• Deposition Author(s): Lim, H.S., Cho, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.296 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Mre11-Rad50-ATP S Complex: Understanding the Interplay between Mre11 and Rad50

Lim, H.S., Kim, J.S., Park, Y.B., Gwon, G.H., Cho, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.68 kDa 
• Atom Count: 5,932 
• Modeled Residue Count: 723 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA double-strand break repair rad50 ATPase	A, B	371	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: rad50, MJ1322
UniProt
Find proteins for Q58718 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58718  Go to UniProtKB:  Q58718

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.296 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.16	α = 90
b = 95.3	β = 90
c = 110.98	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Lim, H.S., Cho, Y.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-23
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary