2H56

Crystal structure of DNA-3-methyladenine glycosidase (10174367) from Bacillus halodurans at 2.55 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2H56/pdb

• Classification: HYDROLASE
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-25 Released: 2006-07-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Crystal structure of DNA-3-methyladenine glycosidase (10174367) from Bacillus halodurans at 2.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.25 kDa 
• Atom Count: 4,855 
• Modelled Residue Count: 639 
• Deposited Residue Count: 699 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-3-methyladenine glycosidase	A, B, C	233	Halalkalibacterium halodurans	Mutation(s): 4  Gene Names: 10174367 EC: 3.2.2
UniProt
Find proteins for Q9KC25 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KC25  Go to UniProtKB:  Q9KC25

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.246 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 6₅
• Diffraction Data: https://doi.org/10.18430/M32H56

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.752	α = 90
b = 141.752	β = 90
c = 85.949	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELX	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations