3AV0 | pdb_00003av0

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.276 (Depositor), 0.275 (DCC)
R-Value Work:
0.214 (Depositor), 0.204 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Models: experimental
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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: 88.95 kDa
Atom Count: 6,094
Modeled Residue Count: 734
Deposited Residue Count: 757
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 EC: 3.1
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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58719
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58718
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], L [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.276 (Depositor), 0.275 (DCC)
R-Value Work: 0.214 (Depositor), 0.204 (DCC)
R-Value Observed: 0.221 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Lim, H.S.

Kim, J.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: Source and taxonomy
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description