5J3E | pdb_00005j3e

Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA

• PDB DOI: https://doi.org/10.2210/pdb5J3E/pdb
• NAKB: 5J3E

• Classification: NUCLEAR PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-30 Released: 2016-04-20 
• Deposition Author(s): Halabelian, L., Tempel, W., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA

Halabelian, L., Tempel, W., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H.

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 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: 66.19 kDa 
• Atom Count: 3,764 
• Modeled Residue Count: 391 
• Deposited Residue Count: 498 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymocyte nuclear protein 1	A, B	225	Homo sapiens	Mutation(s): 0  Gene Names: THYN1, THY28, HSPC144, MDS012, My0054
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P016 (Homo sapiens) Explore Q9P016  Go to UniProtKB:  Q9P016
PHAROS:  Q9P016 GTEx:  ENSG00000151500

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5-methylcytosine containing DNA	C, D, E, F	12	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35J3E

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.327	α = 90
b = 73.232	β = 91.18
c = 108.201	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Halabelian, L., Tempel, W., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description