2H5X | pdb_00002h5x

RuvA from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb2H5X/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2006-05-28 Released: 2006-08-15
Deposition Author(s): Prabu, J.R., Thamotharan, S., Khanduja, J.S., Alipio, E.Z., Kim, C.Y., Waldo, G.S., Terwilliger, T.C., Segelke, B., Lekin, T., Toppani, D., Hung, L.W., Yu, M., Bursey, E., Muniyappa, K., Chandra, N.R., Vijayan, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.272 (Depositor), 0.273 (DCC)
R-Value Work:
0.233 (Depositor), 0.233 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination.

Prabu, J.R., Thamotharan, S., Khanduja, J.S., Alipio, E.Z., Kim, C.Y., Waldo, G.S., Terwilliger, T.C., Segelke, B., Lekin, T., Toppani, D., Hung, L.W., Yu, M., Bursey, E., Muniyappa, K., Chandra, N.R., Vijayan, M.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 731-734

PubMed: 16880543 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309106024791
Primary Citation Related Structures:
2H5X

PubMed Abstract:
The process of recombinational repair is crucial for maintaining genomic integrity and generating biological diversity. In association with RuvB and RuvC, RuvA plays a central role in processing and resolving Holliday junctions, which are a critical intermediate in homologous recombination. Here, the cloning, purification and structure determination of the RuvA protein from Mycobacterium tuberculosis (MtRuvA) are reported. Analysis of the structure and comparison with other known RuvA proteins reveal an octameric state with conserved subunit-subunit interaction surfaces, indicating the requirement of octamer formation for biological activity. A detailed analysis of plasticity in the RuvA molecules has led to insights into the invariant and variable regions, thus providing a framework for understanding regional flexibility in various aspects of RuvA function.

Organizational Affiliation

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Macromolecule Content

Total Structure Weight: 81.22 kDa
Atom Count: 5,559
Modeled Residue Count: 730
Deposited Residue Count: 784
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction ATP-dependent DNA helicase ruvA	A, B, C, D	196	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ruvA EC: 3.6.1
UniProt
Find proteins for P9WGW3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGW3 Go to UniProtKB: P9WGW3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.272 (Depositor), 0.273 (DCC)
R-Value Work: 0.233 (Depositor), 0.233 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.642	α = 90
b = 137.642	β = 90
c = 88.97	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-08-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description