8ECX | pdb_00008ecx

PA0709 with glyoxal and BME modifications

PDB DOI: https://doi.org/10.2210/pdb8ECX/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 3.0 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: 71.58 kDa
Atom Count: 5,916
Modeled Residue Count: 603
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibiotic biosynthesis monooxygenase	A, B, C, D, E A, B, C, D, E, F	102	Pseudomonas aeruginosa	Mutation(s): 0 EC: 1
UniProt
Find proteins for A0A072ZNL3 (Pseudomonas aeruginosa) Explore A0A072ZNL3 Go to UniProtKB: A0A072ZNL3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A072ZNL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
POK Query on POK	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₈ H₁₆ N₄ O₄		ARG

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.189 (Depositor), 0.189 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.013	α = 90
b = 148.984	β = 90
c = 120.184	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Cuthbert, B.J.

Goulding, C.W.

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: 2023-11-15
Changes: Data collection, Derived calculations
Version 2.0: 2023-12-27
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Polymer sequence, Refinement description, Structure summary
Version 3.0: 2024-10-23
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

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PA0709 with glyoxal and BME modifications

Structural characterization of PA0709

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

8ECX | pdb_00008ecx