3S40 | pdb_00003s40

The crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne

• PDB DOI: https://doi.org/10.2210/pdb3S40/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus anthracis str. Sterne
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-18 Released: 2011-06-01 
• Deposition Author(s): Tan, K., Zhang, R., Xu, X., Cui, H., Peterson, S., Savchenko, A., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne

Tan, K., Zhang, R., Xu, X., Cui, H., Peterson, S., Savchenko, A., Anderson, W.F., Joachimiak, A.

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.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 133.48 kDa 
• Atom Count: 8,929 
• Modeled Residue Count: 1,116 
• Deposited Residue Count: 1,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
diacylglycerol kinase	A, B, C, D	304	Bacillus anthracis str. Sterne	Mutation(s): 0  Gene Names: BAS4713, BA_5075, GBAA_5075
UniProt
Find proteins for A0A6L8P1L2 (Bacillus anthracis) Explore A0A6L8P1L2  Go to UniProtKB:  A0A6L8P1L2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.608	α = 90
b = 130.758	β = 115.04
c = 72.794	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Tan, K., Zhang, R., Xu, X., Cui, H., Peterson, S., Savchenko, A., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-09
  Changes: Structure summary