5YO9 | pdb_00005yo9

Crystal structure of KAS III from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb5YO9/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-10-27 Released: 2018-12-05
Deposition Author(s): Lee, W.C., Jung, M., Lee, J., Kim, Y.
Funding Organization(s): National Research Foundation of Korea

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a novel KAS III from Acinetobacter baumannii

Lee, W.C., Jung, M., Lee, J., Kim, Y.

To be published.

Macromolecule Content

Total Structure Weight: 82.62 kDa
Atom Count: 6,096
Modeled Residue Count: 737
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-Oxoacyl-[acyl-carrier-(ACP)] synthase III C terminal family protein	A, B	371	Acinetobacter baumannii	Mutation(s): 1 Gene Names: KAS III EC: 2.3.1.180 (PDB Primary Data), 2.3.1.41 (PDB Primary Data)
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B], E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.211 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.135	α = 90
b = 106.942	β = 90
c = 109.959	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-05

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2018-12-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.