4DC9 | pdb_00004dc9

Hexameric ring of Methanococcus voltae RadA

PDB DOI: https://doi.org/10.2210/pdb4DC9/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Methanococcus voltae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-01-17 Released: 2012-05-02
Deposition Author(s): Du, L., Luo, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.266 (Depositor), 0.263 (DCC)
R-Value Work:
0.206 (Depositor), 0.203 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of a hexameric form of RadA recombinase from Methanococcus voltae.

Du, L., Luo, Y.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 511-516

PubMed: 22691778 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309112010226
Primary Citation Related Structures:
4DC9

PubMed Abstract:
Archaeal RadA proteins are close homologues of eukaryal Rad51 and DMC1 proteins and are remote homologues of bacterial RecA proteins. For the repair of double-stranded breaks in DNA, these recombinases promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. This DNA-repair function also plays a key role in the resistance of cancer cells to chemotherapy and radiotherapy and in the resistance of bacterial cells to antibiotics. A hexameric form of a truncated Methanococcus voltae RadA protein devoid of its small N-terminal domain has been crystallized. The RadA hexamers further assemble into two-ringed assemblies. Similar assemblies can be observed in the crystals of Pyrococcus furiosus RadA and Homo sapiens DMC1. In all of these two-ringed assemblies the DNA-interacting L1 region of each protomer points inward towards the centre, creating a highly positively charged locus. The electrostatic characteristics of the central channels can be utilized in the design of novel recombinase inhibitors.

Organizational Affiliation

Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada.

Macromolecule Content

Total Structure Weight: 177.11 kDa
Atom Count: 12,092
Modeled Residue Count: 1,542
Deposited Residue Count: 1,596
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair and recombination protein radA	A, B, C, D, E A, B, C, D, E, F	266	Methanococcus voltae	Mutation(s): 0 Gene Names: radA
UniProt
Find proteins for O73948 (Methanococcus voltae) Explore O73948 Go to UniProtKB: O73948
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O73948
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.266 (Depositor), 0.263 (DCC)
R-Value Work: 0.206 (Depositor), 0.203 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.351	α = 90
b = 118.577	β = 138.05
c = 141.731	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Du, L.

Luo, Y.

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2013-01-23
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description