7NXG | pdb_00007nxg

Wax synthase 1 from Acinetobacter baylyi (AbWSD1) co-crystallized with myristic acid

PDB DOI: https://doi.org/10.2210/pdb7NXG/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Acinetobacter baylyi ADP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-18 Released: 2022-03-30
Deposition Author(s): Vollheyde, K., Kuehnel, K., Lambrecht, F., Kawelke, S., Herrfurth, C., Feussner, I.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.209 (Depositor), 0.209 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of the Bifunctional Wax Synthase 1 from Acinetobacter baylyi Suggests a Conformational Change upon Substrate Binding and Formation of Additional Substrate Binding Sites

Vollheyde, K., Kuhnel, K., Lambrecht, F., Kawelke, S., Herrfurth, C., Feussner, I.

(2022) ACS Catal 12: 9753-9765

DOI: https://doi.org/10.1021/acscatal.2c01712

Macromolecule Content

Total Structure Weight: 52.59 kDa
Atom Count: 3,312
Modeled Residue Count: 390
Deposited Residue Count: 463
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-acyltransferase WSD	A	463	Acinetobacter baylyi ADP1	Mutation(s): 0 Gene Names: wax-dgaT, ACIAD0832 EC: 2.3.1.20 (PDB Primary Data), 2.3.1.75 (PDB Primary Data)
UniProt
Find proteins for Q8GGG1 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore Q8GGG1 Go to UniProtKB: Q8GGG1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8GGG1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYR (Subject of Investigation/LOI) Query on MYR 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]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-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: 1.95 Å
R-Value Free: 0.209 (Depositor), 0.209 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.32	α = 90
b = 118.32	β = 90
c = 142.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
SHELXCD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-30

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History (Full details and data files)

Version 1.0: 2022-03-30
Type: Initial release
Version 2.0: 2022-10-12
Changes: Atomic model, Database references, Source and taxonomy
Version 2.1: 2024-06-19
Changes: Data collection

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.