7BJQ | pdb_00007bjq

Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex with ssDNA

• PDB DOI: https://doi.org/10.2210/pdb7BJQ/pdb
• NAKB: 7BJQ

• Classification: DNA BINDING PROTEIN
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-14 Released: 2022-07-27 
• Deposition Author(s): De March, M., Onesti, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus

De March, M., Onesti, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.9 kDa 
• Atom Count: 7,031 
• Modeled Residue Count: 914 
• Deposited Residue Count: 952 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved protein	A, B	464	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0  Gene Names: MTH_1422
UniProt
Find proteins for O27473 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27473  Go to UniProtKB:  O27473

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')	C [auth D], D [auth E], E [auth F], F [auth G]	6	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth B], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.08	α = 86.12
b = 69.501	β = 69.26
c = 72.21	γ = 69.53

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): De March, M., Onesti, S.

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description