7WJR | pdb_00007wjr

Crystal structure of dihydroxybenzoate decarboxylase mutant A63S from Aspergillus oryzae in complex with catechol

PDB DOI: https://doi.org/10.2210/pdb7WJR/pdb

Classification: HYDROLASE
Organism(s): Aspergillus oryzae RIB40
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-01-07 Released: 2023-01-18
Deposition Author(s): Yan, F., Song, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.175 (Depositor), 0.150 (DCC)
R-Value Work:
0.144 (Depositor), 0.140 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular mechanism of reversible decarboxylase with efficient CO2 fixation

Yan, F., Song, X.

To be published.

Macromolecule Content

Total Structure Weight: 156.78 kDa
Atom Count: 12,806
Modeled Residue Count: 1,356
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-dihydroxybenzoate decarboxylase	A, B, C, D	339	Aspergillus oryzae RIB40	Mutation(s): 1 EC: 4.1.1.46
UniProt
Find proteins for P80402 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore P80402 Go to UniProtKB: P80402
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80402
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAQ (Subject of Investigation/LOI) Query on CAQ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	CATECHOL C₆ H₆ O₂ YCIMNLLNPGFGHC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]