7YIK | pdb_00007yik

The structure of archaeal nuclease RecJ2 from Methanocaldococcus jannaschii

PDB DOI: https://doi.org/10.2210/pdb7YIK/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-16 Released: 2023-07-19
Deposition Author(s): Wang, W.W., Liu, X.P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.250 (Depositor), 0.249 (DCC)
R-Value Work:
0.195 (Depositor), 0.199 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7YIK

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

Literature

The structure of archaeal nuclease RecJ2 from Methanocaldococcus jannaschii

Wang, W.W., Yi, G.S., Zhou, H., Zhao, Y.X., Wang, Q.S., He, J.H., Yu, F., Xiao, X., Liu, X.P.

To be published.

Macromolecule Content

Total Structure Weight: 97.81 kDa
Atom Count: 7,056
Modeled Residue Count: 860
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nuclease RecJ2	A, B	432	Methanocaldococcus jannaschii DSM 2661	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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.250 (Depositor), 0.249 (DCC)
R-Value Work: 0.195 (Depositor), 0.199 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.522	α = 90
b = 177.818	β = 90
c = 66.297	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32170097
National Natural Science Foundation of China (NSFC)	China	U1832161
National Natural Science Foundation of China (NSFC)	China	41921006

Revision History (Full details and data files)

Version 1.0: 2023-07-19
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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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.