8IK2 | pdb_00008ik2

RhlA exhibits dual thioesterase and acyltransferase activities during rhamnolipid biosynthesis

PDB DOI: https://doi.org/10.2210/pdb8IK2/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-02-28 Released: 2023-11-01
Deposition Author(s): Tang, T., Fu, L.H., Xie, W.H., Luo, Y.Z., Zhang, Y.T., Si, T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.160 (Depositor), 0.161 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8IK2

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

RhlA Exhibits Dual Thioesterase and Acyltransferase Activities during Rhamnolipid Biosynthesis

Tang, T., Fu, L., Xie, W., Luo, Y., Zhang, Y., Zhang, J., Si, T.

(2023) ACS Catal 13: 5759-5766

DOI: https://doi.org/10.1021/acscatal.3c00046

Macromolecule Content

Total Structure Weight: 34.03 kDa
Atom Count: 2,334
Modeled Residue Count: 270
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-(3-hydroxydecanoyloxy)decanoate synthase	A	301	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: rhlA, PA3479 EC: 2.3.1
UniProt
Find proteins for Q51559 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q51559 Go to UniProtKB: Q51559
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q51559
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5UF (Subject of Investigation/LOI) Query on 5UF 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]	(3~{S})-3-oxidanyldecanoic acid C₁₀ H₂₀ O₃ FYSSBMZUBSBFJL-VIFPVBQESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.200 (Depositor), 0.201 (DCC)
R-Value Work: 0.160 (Depositor), 0.161 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.629	α = 90
b = 63.89	β = 90
c = 85.004	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071428

Revision History (Full details and data files)

Version 1.0: 2023-11-01
Type: Initial release

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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.