7RAY | pdb_00007ray

Crystal structure of MBD2 with DNA

• PDB DOI: https://doi.org/10.2210/pdb7RAY/pdb
• NAKB: 7RAY

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-05 Released: 2021-07-21 
• Deposition Author(s): Liu, K., Dong, A., Loppnau, P., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MBD2 with DNA

Liu, K., Dong, A., Loppnau, P., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium (SGC)

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)

Macromolecule Content

• Total Structure Weight: 16.16 kDa 
• Atom Count: 1,138 
• Modelled Residue Count: 98 
• Deposited Residue Count: 103 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-CpG-binding domain protein 2	A	79	Homo sapiens	Mutation(s): 0  Gene Names: MBD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBB5 (Homo sapiens) Explore Q9UBB5  Go to UniProtKB:  Q9UBB5
PHAROS:  Q9UBB5 GTEx:  ENSG00000134046

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*AP*A)-R(P*(5MC))-D(P*GP*TP*TP*GP*GP*C)-3')	B, C	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	D [auth A], E [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.599	α = 90
b = 71.992	β = 90
c = 126.107	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Liu, K., Dong, A., Loppnau, P., Edwards, A.M., Arrowsmith, C.H., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description