6TVV | pdb_00006tvv

Crystal structure of 3'-5' RecJ exonuclease from M. Jannaschii

PDB DOI: https://doi.org/10.2210/pdb6TVV/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-01-10 Released: 2021-01-27
Deposition Author(s): De March, M., Medagli, B., Krastanova, I., Saha, I., Pisani, F., Onesti, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6TVV

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of 3'-5' RecJ exonuclease from M. Jannaschii

De March, M., Medagli, B., Krastanova, I., Saha, I., Pisani, F., Onesti, S.

To be published.

Macromolecule Content

Total Structure Weight: 98.31 kDa
Atom Count: 6,373
Modeled Residue Count: 857
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MjaRecJ	A, B	432	Methanocaldococcus jannaschii	Mutation(s): 0 Gene Names: MJ0831 EC: 3.1
UniProt
Find proteins for Q58241 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58241 Go to UniProtKB: Q58241
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58241
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.264 (Depositor), 0.264 (DCC)
R-Value Work: 0.214 (Depositor), 0.214 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.07	α = 90
b = 92.07	β = 90
c = 275.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.