8H4Q | pdb_00008h4q

Aspergillomarasmine A biosynthese complex with OPS

PDB DOI: https://doi.org/10.2210/pdb8H4Q/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pyrenophora teres f. teres 0-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-11 Released: 2023-10-18
Deposition Author(s): Lu, M., Zhang, J., Wang, Z., Han, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC), National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.233 (Depositor), 0.234 (DCC)
R-Value Work:
0.215 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Investigation of AMA Synthase from Pyrenophora teres f. teres 0-1 for the Synthesis of Aspergillomarasmine A Analogues and Non-Canonical Amino Acids

Zhu, Z., Ma, Y., Xie, X., Wang, Z., Han, L., Song, J., Liang, Y., Poelarends, G.J., Chen, Y., Lu, M., Zhang, J.

(2024) Adv Synth Catal 366: 5160-5170

DOI: https://doi.org/10.1002/adsc.202401118

Macromolecule Content

Total Structure Weight: 116.32 kDa
Atom Count: 7,539
Modelled Residue Count: 969
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodanese domain-containing protein	A [auth N], B [auth A]	525	Pyrenophora teres f. teres 0-1	Mutation(s): 0 Gene Names: PTT_12124
UniProt
Find proteins for E3RT21 (Pyrenophora teres f. teres (strain 0-1)) Explore E3RT21 Go to UniProtKB: E3RT21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E3RT21
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P1T (Subject of Investigation/LOI) Query on P1T Download Ideal Coordinates CCD File SDF format, chain C [auth N] SDF format, chain D [auth A] MOL2 format, chain C [auth N] MOL2 format, chain D [auth A] mmCIF format, chain C [auth N] mmCIF format, chain D [auth A]	C [auth N], D [auth A]	2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID C₁₁ H₁₅ N₂ O₇ P BXUDKFHCAMQSRX-UHFFFAOYSA-N		Interactions Focus chain C [auth N] Focus chain D [auth A] Interactions & Density Focus chain C [auth N] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.233 (Depositor), 0.234 (DCC)
R-Value Work: 0.215 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.125	α = 90
b = 264.071	β = 90
c = 163.897	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82003627
National Science Foundation (NSF, China)	China	BK20200565

Revision History (Full details and data files)

Version 1.0: 2023-10-18
Type: Initial release
Version 1.1: 2025-04-30
Changes: Database references, Structure summary

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.