8H41

Crystal structure of a decarboxylase from Trichosporon moniliiforme in complex with o-nitrophenol

• PDB DOI: https://doi.org/10.2210/pdb8H41/pdb

• Classification: HYDROLASE
• Organism(s): Cutaneotrichosporon moniliiforme
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-09 Released: 2023-08-16 
• Deposition Author(s): Gao, J., Zhao, Y.P., Li, Q., Liu, W.D., Sheng, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Literature

A Combined Computational-Experimental Study on the Substrate Binding and Reaction Mechanism of Salicylic Acid Decarboxylase

Chen, F., Zhao, Y., Zhang, C., Wang, W., Gao, J., Li, Q., Qin, H., Dai, Y., Liu, W., Liu, F., Su, H., Sheng, X.

(2022) Catalysts 12

• DOI: https://doi.org/10.3390/catal12121577

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.3 kDa 
• Atom Count: 6,565 
• Modelled Residue Count: 709 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Salicylate decarboxylase	A, B	358	Cutaneotrichosporon moniliiforme	Mutation(s): 0  Gene Names: sdc EC: 4.1.1.91
UniProt
Find proteins for P0CT50 (Cutaneotrichosporon moniliiforme) Explore P0CT50  Go to UniProtKB:  P0CT50

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OPO (Subject of Investigation/LOI)	C [auth A], E [auth B]	O-NITROPHENOL C6 H5 N O3 IQUPABOKLQSFBK-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.916	α = 90
b = 92.31	β = 90
c = 128.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Gao, J., Zhao, Y.P., Li, Q., Liu, W.D., Sheng, X.

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

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release