3ID9 | pdb_00003id9

Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis

• PDB DOI: https://doi.org/10.2210/pdb3ID9/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thuringiensis str. Al Hakam
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-20 Released: 2009-09-08 
• Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis

Palani, K., Burley, S.K., Swaminathan, S.

To be published.

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: 39.87 kDa 
• Atom Count: 2,114 
• Modeled Residue Count: 251 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MutT/NUDIX family protein	A, B	171	Bacillus thuringiensis str. Al Hakam	Mutation(s): 0  Gene Names: BALH_3260

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	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:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.494	α = 90
b = 115.494	β = 90
c = 106.075	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary