8X4Q

Apo structure of L-tryptophan specific decarboxylase PsiD

PDB DOI: https://doi.org/10.2210/pdb8X4Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Psilocybe cubensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-11-15 Released: 2024-11-20
Deposition Author(s): Meng, C.Y., Wen, Y., Guo, W.T., Wu, B.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.222
R-Value Work: 0.172
R-Value Observed: 0.175

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

This is version 1.0 of the entry. See complete history.

Literature

Apo structure of L-tryptophan specific decarboxylase PsiD

Meng, C.Y., Wen, Y., Guo, W.T., Wu, B.X.

To be published.

Macromolecule Content

Total Structure Weight: 298.24 kDa
Atom Count: 19,055
Modelled Residue Count: 2,290
Deposited Residue Count: 2,634
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-tryptophan decarboxylase	A B [auth C] C [auth E] D [auth G] E [auth I] A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	402	Psilocybe cubensis	Mutation(s): 0 Gene Names: psiD EC: 4.1.1.105
UniProt
Find proteins for P0DPA6 (Psilocybe cubensis) Explore P0DPA6 Go to UniProtKB: P0DPA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DPA6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-tryptophan decarboxylase	G [auth L] H [auth J] I [auth H] J [auth F] K [auth D] G [auth L], H [auth J], I [auth H], J [auth F], K [auth D], L [auth B]	37	Psilocybe cubensis	Mutation(s): 1 Gene Names: psiD EC: 4.1.1.105
UniProt
Find proteins for P0DPA6 (Psilocybe cubensis) Explore P0DPA6 Go to UniProtKB: P0DPA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DPA6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.222
R-Value Work: 0.172
R-Value Observed: 0.175
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.285	α = 90
b = 120.763	β = 99.432
c = 128.456	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-11-20
Type: Initial release

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.