6A9N | pdb_00006a9n

Crystal structure of KAS III from Propionibacterium acnes

PDB DOI: https://doi.org/10.2210/pdb6A9N/pdb

Classification: TRANSFERASE
Organism(s): Cutibacterium acnes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-07-14 Released: 2019-07-17
Deposition Author(s): Lee, W.C., Cheon, D., Kim, Y.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.209 (Depositor), 0.206 (DCC)
R-Value Work:
0.177 (Depositor), 0.174 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6A9N

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of KAS III from Propionibacterium acnes

Cheon, D., Lee, W.C., Kim, Y.

To be published.

Macromolecule Content

Total Structure Weight: 71.17 kDa
Atom Count: 5,344
Modeled Residue Count: 662
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3	A, B	333	Cutibacterium acnes	Mutation(s): 1 Gene Names: fabH, B1B09_02220 EC: 2.3.1.180 (PDB Primary Data), 2.3.1.300 (UniProt)
UniProt
Find proteins for P0DW99 (Cutibacterium acnes) Explore P0DW99 Go to UniProtKB: P0DW99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DW99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.209 (Depositor), 0.206 (DCC)
R-Value Work: 0.177 (Depositor), 0.174 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.518	α = 90
b = 105.518	β = 90
c = 326.933	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	MSIP-2016R1A2B2008543

Revision History (Full details and data files)

Version 1.0: 2019-07-17
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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