4B21

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

• PDB DOI: https://doi.org/10.2210/pdb4B21/pdb
• NAKB: 4B21

• Classification: HYDROLASE/DNA
• Organism(s): Schizosaccharomyces pombe, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-12 Released: 2013-01-09 
• Deposition Author(s): Dalhus, B., Nilsen, L., Korvald, H., Huffman, J., Forstrom, R.J., McMurray, C.T., Alseth, I., Tainer, J.A., Bjoras, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.221 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.14 kDa 
• Atom Count: 2,388 
• Modelled Residue Count: 229 
• Deposited Residue Count: 253 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2	A	232	Schizosaccharomyces pombe	Mutation(s): 0  EC: 3.2.2.21
UniProt
Find proteins for O94468 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O94468  Go to UniProtKB:  O94468

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3'	B [auth X]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'	C [auth Y]	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	E [auth A], F [auth A], G [auth Y]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.221 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.926	α = 90
b = 84.746	β = 90
c = 126.713	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Dalhus, B., Nilsen, L., Korvald, H., Huffman, J., Forstrom, R.J., McMurray, C.T., Alseth, I., Tainer, J.A., Bjoras, M.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary