3AV0

Crystal structure of Mre11-Rad50 bound to ATP S

• PDB DOI: https://doi.org/10.2210/pdb3AV0/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., Kim, J.S., Cho, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.276 
• R-Value Work: 0.214 
• R-Value Observed: 0.221 

Starting Models: 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: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 88.95 kDa 
• Atom Count: 6,094 
• Modelled Residue Count: 734 
• Deposited Residue Count: 757 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA double-strand break repair protein mre11	A	386	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: rad50, MJ1322
UniProt
Find proteins for Q58719 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58719  Go to UniProtKB:  Q58719

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA double-strand break repair rad50 ATPase	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	G [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	D [auth A], F [auth B], L [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
MG	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.276 
• R-Value Work: 0.214 
• R-Value Observed: 0.221 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.958	α = 90
b = 147.129	β = 90
c = 175.907	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Lim, H.S., Kim, J.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: Source and taxonomy
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description