3SMD | pdb_00003smd

Crystal structure of a mut/nudix family protein from bacillus thuringiensis

• PDB DOI: https://doi.org/10.2210/pdb3SMD/pdb
• Entry: 3SMD supersedes: 3EDS

• Classification: Structural Genomics, Unknown Function
• Organism(s): Bacillus thuringiensis str. Al Hakam
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-27 Released: 2011-07-20 
• Deposition Author(s): Palani, K., Kumaran, D., 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: 1.76 Å
• R-Value Free: 
  0.259 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of a mut/nudix family protein from bacillus thuringiensis

Palani, K., Kumaran, D., Burley, S.K., Swaminathan, S.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.59 kDa 
• Atom Count: 1,208 
• Modeled Residue Count: 133 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MutT/NUDIX family protein	A	153	Bacillus thuringiensis str. Al Hakam	Mutation(s): 0  Gene Names: balh_2480

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.259 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64	α = 90
b = 64	β = 90
c = 59.01	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Palani, K., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)
• This entry supersedes: 3EDS

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary