6CNG | pdb_00006cng

The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B3 protein loaded with linoleic acid to 1.47 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6CNG/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae R6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-03-08 Released: 2019-07-03
Deposition Author(s): Cuypers, M.G., Subramanian, C., White, S.W., Rock, C.O.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.165 (Depositor), 0.163 (DCC)
R-Value Work:
0.137 (Depositor), 0.138 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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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 the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B3 protein loaded with linoleic acid to 1.47 Angstrom resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 67.83 kDa
Atom Count: 5,262
Modeled Residue Count: 562
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty Acid Kinase (Fak) B3 protein	A, B [auth D]	301	Streptococcus pneumoniae R6	Mutation(s): 0 Gene Names: spr0652
UniProt
Find proteins for Q8DQI6 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DQI6 Go to UniProtKB: Q8DQI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DQI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EIC Query on EIC Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain C [auth A] MOL2 format, chain K [auth D] MOL2 format, chain C [auth A] mmCIF format, chain K [auth D] mmCIF format, chain C [auth A]	C [auth A], K [auth D]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain C [auth A] Focus chain K [auth D] Interactions & Density Focus chain C [auth A] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] M [auth D] E [auth A], F [auth A], G [auth A], H [auth A], M [auth D], N [auth D], O [auth D], P [auth D], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], V [auth D], W [auth D], X [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain D [auth A] MOL2 format, chain L [auth D] MOL2 format, chain D [auth A] mmCIF format, chain L [auth D] mmCIF format, chain D [auth A]	D [auth A], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth D] Interactions & Density Focus chain D [auth A] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.165 (Depositor), 0.163 (DCC)
R-Value Work: 0.137 (Depositor), 0.138 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.775	α = 90
b = 103.414	β = 112.99
c = 67.469	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2019-07-03
Type: Initial release
Version 1.1: 2019-12-04
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description