8G3J | pdb_00008g3j

Non-ribosomal PCP-C didomain R2577G (thioether stabilised glycolic acid) acceptor bound state

PDB DOI: https://doi.org/10.2210/pdb8G3J/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-02-08 Released: 2023-06-14
Deposition Author(s): Ho, Y.T.C., Izore, T., Cryle, M.J.
Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.243 (Depositor), 0.241 (DCC)
R-Value Work:
0.201 (Depositor), 0.203 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Exploring the selectivity and engineering potential of an NRPS condensation domain involved in the biosynthesis of the thermophilic siderophore fuscachelin

Ho, Y.T.C., Izore, T., Kaczmarski, J.A., Marschall, E., Ratnayake, M., Tailhades, J., Steer, D.L., Schittenhelm, R.B., Tosin, M., Jackson, C.J., Cryle, M.J.

(2023) Front Catal 3

DOI: https://doi.org/10.3389/fctls.2023.1184959

Macromolecule Content

Total Structure Weight: 115.58 kDa
Atom Count: 8,259
Modeled Residue Count: 1,018
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCP-C didomain	A, B	528	Thermobifida fusca YX	Mutation(s): 1 Gene Names: Tfu_1867
UniProt
Find proteins for Q47NR9 (Thermobifida fusca (strain YX)) Explore Q47NR9 Go to UniProtKB: Q47NR9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q47NR9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YJI (Subject of Investigation/LOI) Query on YJI Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2-hydroxyethyl)sulfanyl]ethyl}-beta-alaninamide C₁₃ H₂₇ N₂ O₈ P S IGYAFBQHDWNTQK-NSHDSACASA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.243 (Depositor), 0.241 (DCC)
R-Value Work: 0.201 (Depositor), 0.203 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.117	α = 90
b = 105.278	β = 90
c = 106.904	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP190101272
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1140619

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-12-27
Changes: Data collection, Database references
Version 1.2: 2024-10-30
Changes: Database references, Structure summary

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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.