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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.238 (Depositor), 0.233 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L8P1L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.233 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (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

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Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.