3T5P

Crystal structure of a putative diacylglycerol kinase from Bacillus anthracis str. Sterne

• PDB DOI: https://doi.org/10.2210/pdb3T5P/pdb

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


• Deposited: 2011-07-27 Released: 2011-09-07 
• Deposition Author(s): Hou, J., Zheng, H., Chruszcz, M., Cooper, D.R., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.241 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Crystal structure of a putative diacylglycerol kinase from Bacillus anthracis str. Sterne

Hou, J., Zheng, H., Chruszcz, M., Cooper, D.R., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 405.18 kDa 
• Atom Count: 26,322 
• Modelled Residue Count: 3,448 
• Deposited Residue Count: 3,672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BmrU protein	A, B, C, D, E, F, G, H, I, J, K, L	306	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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.241 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M35K57

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.016	α = 90
b = 115.1	β = 92.34
c = 208.018	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Hou, J., Zheng, H., Chruszcz, M., Cooper, D.R., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary