8ECP | pdb_00008ecp

R16A PA0709 with BME modifications

PDB DOI: https://doi.org/10.2210/pdb8ECP/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-09-02 Released: 2023-09-27
Deposition Author(s): Cuthbert, B.J., Goulding, C.W., Ulijasz, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.205 (Depositor), 0.206 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Structural characterization of PA0709

Cuthbert, B.J., Goulding, C.W., Ulijasz, A.T.

To be published.

Macromolecule Content

Total Structure Weight: 24.74 kDa
Atom Count: 1,937
Modeled Residue Count: 195
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibiotic biosynthesis monooxygenase	A, B	102	Pseudomonas aeruginosa	Mutation(s): 1 EC: 1
UniProt
Find proteins for A0A072ZNL3 (Pseudomonas aeruginosa) Explore A0A072ZNL3 Go to UniProtKB: A0A072ZNL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A072ZNL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A], I [auth A], N [auth B], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain P [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] G [auth A] H [auth A] J [auth A] C [auth A], D [auth A], G [auth A], H [auth A], J [auth A], K [auth A], M [auth B], O [auth B], Q [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain Q [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.205 (Depositor), 0.206 (DCC)
R-Value Work: 0.176 (Depositor), 0.177 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.783	α = 90
b = 62.783	β = 90
c = 120.367	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-09-27
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary
Version 1.2: 2026-03-04
Changes: 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.