8X0O | pdb_00008x0o

Crystal structure of Tyrosine decarboxylase H203F mutant in complex with the cofactor PLP and Tyrosine

PDB DOI: https://doi.org/10.2210/pdb8X0O/pdb

Classification: LYASE
Organism(s): Papaver somniferum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-11-05 Released: 2025-02-12
Deposition Author(s): Wang, H., Yu, J., Yao, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.279 (Depositor), 0.277 (DCC)
R-Value Work:
0.234 (Depositor), 0.233 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Tyrosine decarboxylase H203F mutant in complex with the cofactor PLP and Tyrosine

Wang, H., Yu, J., Yao, M.

To be published.

Macromolecule Content

Total Structure Weight: 358.69 kDa
Atom Count: 22,938
Modeled Residue Count: 2,889
Deposited Residue Count: 3,186
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine/DOPA decarboxylase 2	A, B, C, D, E A, B, C, D, E, F	531	Papaver somniferum	Mutation(s): 1 Gene Names: TYDC2 EC: 4.1.1.25 (UniProt), 4.1.1.28 (UniProt)
UniProt
Find proteins for P54769 (Papaver somniferum) Explore P54769 Go to UniProtKB: P54769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TYR (Subject of Investigation/LOI) Query on TYR Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], I [auth C], J [auth D]	TYROSINE C₉ H₁₁ N O₃ OUYCCCASQSFEME-QMMMGPOBSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.279 (Depositor), 0.277 (DCC)
R-Value Work: 0.234 (Depositor), 0.233 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.55	α = 90
b = 118.5	β = 90
c = 181.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17H05424
Japan Society for the Promotion of Science (JSPS)	Japan	19H04633

Revision History (Full details and data files)

Version 1.0: 2025-02-12
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.