5ZE0

Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 

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
mouse RAG1
A, C
627Mus musculusGene Names: Rag1
EC: 3.1.-.-, 2.3.2.27
Find proteins for P15919 (Mus musculus)
Go to UniProtKB:  P15919
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
mouse RAG2
B, D
389Mus musculusMutations: V3M
Gene Names: Rag2 (Rag-2)
Find proteins for P21784 (Mus musculus)
Go to UniProtKB:  P21784
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HMGB1 A-B box
N
163Mus musculusGene Names: Hmgb1 (Hmg-1, Hmg1)
Find proteins for P63158 (Mus musculus)
Go to UniProtKB:  P63158
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (45-MER)F45synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')I16synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')J16synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (54-MER)G54synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
DNA (30-MER)L30synthetic construct
Entity ID: 9
MoleculeChainsLengthOrganism
DNA (39-MER)M39synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
ethane-1,2-diol
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 132.440α = 90.00
b = 109.030β = 114.43
c = 156.850γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
NIHUnited States--

Revision History 

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