3AUY

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.296
R-Value Work: 0.228
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q58718
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.296
R-Value Work: 0.228
R-Value Observed: 0.228
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Lim, H.S.

Cho, Y.

Revision History (Full details and data files)

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

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Help and Resources

3AUY

Crystal structure of Rad50 bound to ADP

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)