6DKE

The X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with palmitic acid (C16:0) to 1.76 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6DKE/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-29 Released: 2019-05-29
Deposition Author(s): Cuypers, M.G., Subramanian, C., White, S.W., Rock, C.O.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The X-ray crystal structure of Streptococcus pneumoniae Fatty Acid Kinase (Fak) B1 protein loaded with palmitic acid (C16:0) to 1.76 Angstrom resolution

Cuypers, M.G., Subramanian, C., White, S.W., Rock, C.O.

To be published.

Macromolecule Content

Total Structure Weight: 34.79 kDa
Atom Count: 2,514
Modelled Residue Count: 283
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty Acid Kinase (Fak) B1 protein	A	316	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for Q8DP17 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DP17 Go to UniProtKB: Q8DP17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DP17
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.825	α = 90
b = 62.337	β = 95.94
c = 50.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-29

Deposition Author(s):

Subramanian, C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2019-05-29
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2024-03-13
Changes: Data collection, Database references

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.