7MKV

Engineered PLP-dependent decarboxylative aldolase from Aspergillus flavus, UstD2.0, bound as the internal aldimine

PDB DOI: https://doi.org/10.2210/pdb7MKV/pdb

Classification: LYASE, TRANSFERASE
Organism(s): Aspergillus flavus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-04-27 Released: 2022-05-04
Deposition Author(s): Ellis, J.M., Buller, A.R., Bingman, C.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.246
R-Value Work: 0.214
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Biocatalytic synthesis of non-standard amino acids by a decarboxylative aldol reaction

Ellis, J.M., Campbell, M.E., Kumar, P., Geunes, E.P., Bingman, C.A., Buller, A.R.

(2022) Nat Catal 5: 136-143

DOI: https://doi.org/10.1038/s41929-022-00743-0

Macromolecule Content

Total Structure Weight: 148.79 kDa
Atom Count: 9,782
Modelled Residue Count: 1,220
Deposited Residue Count: 1,341
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase-like protein ustD	A, B, C	447	Aspergillus flavus	Mutation(s): 6 Gene Names: ustD, AFLA_095040 EC: 2
UniProt
Find proteins for B8NM72 (Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167)) Explore B8NM72 Go to UniProtKB: B8NM72
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8NM72
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B, C	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS
LLP Query on LLP	A, B, C	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.246
R-Value Work: 0.214
R-Value Observed: 0.215
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.09	α = 90
b = 162.09	β = 90
c = 221.005	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2-GM137417

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release

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 R01GM133198.