1RMD | pdb_00001rmd

RAG1 DIMERIZATION DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1RMD/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-01-10 Released: 1997-07-23 
• Deposition Author(s): Bellon, S.F., Rodgers, K.K., Schatz, D.G., Coleman, J.E., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.257 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster.

Bellon, S.F., Rodgers, K.K., Schatz, D.G., Coleman, J.E., Steitz, T.A.

(1997) Nat Struct Biol 4: 586-591

• PubMed: 9228952 
• DOI: https://doi.org/10.1038/nsb0797-586
• Primary Citation Related Structures: 
  1RMD


• PubMed Abstract: 
  

  The crystal structure of the dimerization domain of the V(D)J recombination-activating protein, RAG1, was solved using zinc anomalous scattering. The structure reveals an unusual combination of multi-class zinc-binding motifs, including a zinc RING finger and a C2H2 zinc finger, that together from a single structural domain. The domain also contains a unique zinc binuclear cluster in place of a normally mononuclear zinc site in the RING finger. Together, four zinc ions help organize the entire domain, including the two helices that form the dimer interface.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.41 kDa 
• Atom Count: 967 
• Modeled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAG1	A	116	Mus musculus	Mutation(s): 0  EC: 3.1 (UniProt), 2.3.2.27 (UniProt)
UniProt
Find proteins for P15919 (Mus musculus) Explore P15919  Go to UniProtKB:  P15919

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.257 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.58	α = 90
b = 57.58	β = 90
c = 98.43	γ = 120

Software Package:

Software Name	Purpose
BAZFAZ	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
BAZFAZ	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-07-23 
Deposition Author(s): Bellon, S.F., Rodgers, K.K., Schatz, D.G., Coleman, J.E., Steitz, T.A.

Revision History  

• Version 1.0: 1997-07-23
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary