8H41 | pdb_00008h41

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.166 (Depositor), 0.168 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CT50
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OPO (Subject of Investigation/LOI) Query on OPO 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]	O-NITROPHENOL C₆ H₅ N O₃ IQUPABOKLQSFBK-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]
MG (Subject of Investigation/LOI) Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.194 (Depositor), 0.195 (DCC)
R-Value Work: 0.166 (Depositor), 0.168 (DCC)
R-Value Observed: 0.167 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2026-03-11
Changes: Refinement description, 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.