8H4H | pdb_00008h4h

The apo structure of Aspergillomarasmine A synthetase

PDB DOI: https://doi.org/10.2210/pdb8H4H/pdb

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

Deposited: 2022-10-10 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: 2.30 Å
R-Value Free:
0.260 (Depositor), 0.256 (DCC)
R-Value Work:
0.240 (Depositor), 0.240 (DCC)
R-Value Observed:
0.240 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8H4H

This is version 2.0 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: 117.8 kDa
Atom Count: 7,466
Modeled Residue Count: 959
Deposited Residue Count: 1,062
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodanese domain-containing protein	A [auth N], B [auth A]	531	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E3RT21
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A [auth N], B [auth A]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.260 (Depositor), 0.256 (DCC)
R-Value Work: 0.240 (Depositor), 0.240 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.89	α = 90
b = 264.099	β = 90
c = 163.368	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

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 2.0: 2025-04-30
Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, 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.