8DL5 | pdb_00008dl5

Crystal structure of PLP-dependent Mannich cyclase LolT

PDB DOI: https://doi.org/10.2210/pdb8DL5/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Penicillium expansum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-06 Released: 2023-06-14
Deposition Author(s): Gao, J., Hai, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.233 (Depositor), 0.230 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A pyridoxal 5'-phosphate-dependent Mannich cyclase.

Gao, J., Liu, S., Zhou, C., Lara, D., Zou, Y., Hai, Y.

(2023) Nat Catal

DOI: https://doi.org/10.1038/s41929-023-00963-y

Macromolecule Content

Total Structure Weight: 111.25 kDa
Atom Count: 6,655
Modeled Residue Count: 811
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase, class V/Cysteine desulfurase	A, B	496	Penicillium expansum	Mutation(s): 0 Gene Names: PEX2_110450
UniProt
Find proteins for A0A0A2J6G6 (Penicillium expansum) Explore A0A0A2J6G6 Go to UniProtKB: A0A0A2J6G6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A2J6G6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.233 (Depositor), 0.230 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.837	α = 90
b = 77.837	β = 90
c = 298.842	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-04-03
Changes: Refinement description

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.