7MKV | pdb_00007mkv

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.215 (Depositor)

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
Modeled 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 (Depositor), 0.250 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (DCC)
R-Value Observed: 0.215 (Depositor)

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.