2B21 | pdb_00002b21

RADA Recombinase in complex with AMPPNP at pH 6.0

• PDB DOI: https://doi.org/10.2210/pdb2B21/pdb

• Classification: RECOMBINATION
• Organism(s): Methanococcus voltae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-09-16 Released: 2006-08-29 
• Deposition Author(s): Qian, X., He, Y., Wu, Y., Luo, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Methanococcus Voltae Rada at an Acidic pH

Qian, X., He, Y., Wu, Y., Luo, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.87 kDa 
• Atom Count: 2,408 
• Modeled Residue Count: 299 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair and recombination protein radA	A	322	Methanococcus voltae	Mutation(s): 1  Gene Names: radA
UniProt
Find proteins for O73948 (Methanococcus voltae) Explore O73948  Go to UniProtKB:  O73948

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	G [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
K	D [auth A], E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.071	α = 90
b = 83.071	β = 90
c = 107.168	γ = 120

Software Package:

Software Name	Purpose
SAINTPLUS	data collection
LSCALE	data reduction
AMoRE	phasing
CNS	refinement
SAINT	data reduction
LSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Qian, X., He, Y., Wu, Y., Luo, Y.

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description