7WMB | pdb_00007wmb

Crystal structure of 2,3-dihydroxybenzoate decarboxylase mutant W23Y from Aspergillus oryzae in complex with catechol

PDB DOI: https://doi.org/10.2210/pdb7WMB/pdb

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

Deposited: 2022-01-14 Released: 2023-01-25
Deposition Author(s): Fan, Y., Xue, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.208 (Depositor), 0.188 (DCC)
R-Value Work:
0.159 (Depositor)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase

Fan, Y., Wu, S., Shi, J., Li, X., Yang, Y., Feng, Y., Xue, S.

(2023) Appl Microbiol Biotechnol 107: 7451-7462

DOI: https://doi.org/10.1007/s00253-023-12813-9

Macromolecule Content

Total Structure Weight: 78.31 kDa
Atom Count: 5,952
Modeled Residue Count: 678
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A, B	339	Aspergillus oryzae	Mutation(s): 1 Gene Names: OAory_01010140 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	CATECHOL C₆ H₆ O₂ YCIMNLLNPGFGHC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.208 (Depositor), 0.188 (DCC)
R-Value Work: 0.159 (Depositor)
R-Value Observed: 0.162 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.711	α = 90
b = 99.711	β = 90
c = 129.675	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21877110

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-01-03
Changes: Database references, 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.