3T5P | pdb_00003t5p

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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BmrU protein	A, B, C, D, E 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
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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain X [auth L] SDF format, chain W [auth K] SDF format, chain V [auth J] SDF format, chain U [auth I] SDF format, chain T [auth H] SDF format, chain S [auth G] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain X [auth L] MOL2 format, chain W [auth K] MOL2 format, chain V [auth J] MOL2 format, chain U [auth I] MOL2 format, chain T [auth H] MOL2 format, chain S [auth G] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain X [auth L] mmCIF format, chain W [auth K] mmCIF format, chain V [auth J] mmCIF format, chain U [auth I] mmCIF format, chain T [auth H] mmCIF format, chain S [auth G] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] 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		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth K] Focus chain X [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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 (Depositor)
R-Value Work: 0.205 (Depositor)
R-Value Observed: 0.207 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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
Version 1.3: 2024-11-20
Changes: Data collection, Structure summary