7YOR | pdb_00007yor

Recj2 and dCMP complex from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb7YOR/pdb

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


• Deposited: 2022-08-02 Released: 2023-08-02 
• 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: 2.53 Å
• R-Value Free: 
  0.253 (Depositor) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

The structure of 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 98.87 kDa 
• Atom Count: 6,955 
• Modeled Residue Count: 861 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
archaeal nuclease RecJ2	A, B	434	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IY9 (Subject of Investigation/LOI)	C [auth A], E [auth B]	[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-furan-2-yl]methyl dihydrogen phosphate C9 H10 N3 O7 P ZPERLPSVNPNRDZ-UHFFFAOYSA-N
EDO	D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.253 (Depositor) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.6	α = 90
b = 175.17	β = 90
c = 66.18	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Wang, W.W., Liu, X.P.

---

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  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary