6CIK

Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cracking the DNA Code for V(D)J Recombination.

Kim, M.S.Chuenchor, W.Chen, X.Cui, Y.Zhang, X.Zhou, Z.H.Gellert, M.Yang, W.

(2018) Mol. Cell 70: 358-370.e4


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
V(D)J recombination-activating protein 1
A, C
625Mus musculusMutations: Q579E
Gene Names: Rag1
EC: 3.1.-.-, 2.3.2.27
Find proteins for P15919 (Mus musculus)
Go to UniProtKB:  P15919
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V(D)J recombination-activating protein 2
B, D
359Mus musculusGene Names: Rag2 (Rag-2)
Find proteins for P21784 (Mus musculus)
Go to UniProtKB:  P21784
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
High mobility group protein B1
N
163Homo sapiensGene Names: HMGB1 (HMG1)
Find proteins for P09429 (Homo sapiens)
Go to Gene View: HMGB1
Go to UniProtKB:  P09429
Entity ID: 4
MoleculeChainsLengthOrganism
Intact 12RSS substrate reverse strandF39Homo sapiens
Entity ID: 5
MoleculeChainsLengthOrganism
Intact 12RSS substrate forward strandI40Homo sapiens
Entity ID: 6
MoleculeChainsLengthOrganism
Nicked 23RSS intermediate reverse strandG55Homo sapiens
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')J15Homo sapiens
Entity ID: 8
MoleculeChainsLengthOrganism
Nicked 23RSS intermediate forward strandM40Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.423α = 90.00
b = 123.149β = 105.03
c = 186.327γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institute of Diabetes and Digestive and Kidney DiseasesUnited StatesDK036147, DK036144, DK036167
National Institutes of Health Intramural AIDS targeted Anti-viral ProgramUnited States--

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references