7CWY | pdb_00007cwy

Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP

PDB DOI: https://doi.org/10.2210/pdb7CWY/pdb

Classification: LYASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-01 Released: 2021-09-01
Deposition Author(s): Yu, X., Gong, M., Huang, J., Liu, W., Chen, C., Guo, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.248 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.207 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP

Yu, X., Gong, M., Huang, J., Liu, W., Chen, C., Guo, R.

To be published.

Macromolecule Content

Total Structure Weight: 211.09 kDa
Atom Count: 14,452
Modeled Residue Count: 1,799
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decarboxylase	A, B, C	620	Enterococcus faecalis	Mutation(s): 0 Gene Names: tyrDC, ddc, ELS84_1624, KUB3007_C03520, NCTC8729_00604 EC: 4.1.1.86 (PDB Primary Data), 4.1.1.25 (UniProt), 4.1.1 (UniProt)
UniProt
Find proteins for Q838D6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838D6 Go to UniProtKB: Q838D6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q838D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.248 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.207 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.527	α = 90
b = 132.527	β = 90
c = 390.13	γ = 120

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

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-01
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.