7BK9 | pdb_00007bk9

Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa in complex with DDD00078426

PDB DOI: https://doi.org/10.2210/pdb7BK9/pdb

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

Deposited: 2021-01-15 Released: 2022-03-02
Deposition Author(s): Moynie, L., Naismith, J.H., Robinson, D.A.
Funding Organization(s): European Communitys Seventh Framework Programme

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.226 (Depositor), 0.235 (DCC)
R-Value Work:
0.199 (Depositor), 0.207 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structures of 3-hydroxydecanoyl-acyl carrier protein dehydratase (FabA) from Pseudomonas aeruginosa

Naismith, J.H., Moynie, L., Robinson, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 95.65 kDa
Atom Count: 6,736
Modeled Residue Count: 834
Deposited Residue Count: 855
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase	A, B, C [auth D], D [auth C], E	171	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: fabA, PA1610 EC: 4.2.1.59 (PDB Primary Data), 5.3.3.14 (PDB Primary Data)
UniProt
Find proteins for O33877 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore O33877 Go to UniProtKB: O33877
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O33877
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U0W (Subject of Investigation/LOI) Query on U0W Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A] G [auth B] H [auth B] I [auth B] J [auth D] F [auth A], G [auth B], H [auth B], I [auth B], J [auth D], K [auth D], L [auth E]	5-[(2,3-Dihydro-1H-inden-5-yloxy)methyl]-2-furoic acid C₁₅ H₁₄ O₄ BQKLXOGKDTYPRT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.226 (Depositor), 0.235 (DCC)
R-Value Work: 0.199 (Depositor), 0.207 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.64	α = 90
b = 143.5	β = 114.08
c = 77.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
DIALS	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: 2022-03-02

Deposition Author(s):

Funding Organization	Location	Grant Number
European Communitys Seventh Framework Programme		--

Revision History (Full details and data files)

Version 1.0: 2022-03-02
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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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.