7XIN

Crystal structure of DODC from Pseudomonas

• PDB DOI: https://doi.org/10.2210/pdb7XIN/pdb

• Classification: LYASE
• Organism(s): Pseudomonas
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-04-13 Released: 2023-04-19 
• Deposition Author(s): Li, X., Zhou, Y.L., Liao, L.J., Liu, X.K., Liu, B., Guo, Y., Feng, Z., Sun, D.Y., Zeng, Z.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.521 
• R-Value Work: 0.473 
• R-Value Observed: 0.475 

Literature

Crystal structure of DODC from Pseudomonas

Li, X., Zhou, Y.L., Liao, L.J., Liu, X.K., Liu, B., Guo, Y., Feng, Z., Sun, D.Y., Zeng, Z.X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 157.4 kDa 
• Atom Count: 10,953 
• Modelled Residue Count: 1,410 
• Deposited Residue Count: 1,428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DOPA decarboxylase	A, B [auth C], C [auth E]	476	Pseudomonas	Mutation(s): 0  EC: 4.1.1.28
UniProt
Find proteins for Q88JU5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JU5  Go to UniProtKB:  Q88JU5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	D [auth A], E [auth C], F [auth E]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.521 
• R-Value Work: 0.473 
• R-Value Observed: 0.475 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.767	α = 90.27
b = 67.014	β = 92.38
c = 168.576	γ = 90.36

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Li, X., Zhou, Y.L., Liao, L.J., Liu, X.K., Liu, B., Guo, Y., Feng, Z., Sun, D.Y., Zeng, Z.X.

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

Revision History  

• Version 1.0: 2023-04-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description