7JPJ

Crystal Structure of the essential dimeric LYSA from Phaeodactylum tricornutum

• PDB DOI: https://doi.org/10.2210/pdb7JPJ/pdb

• Classification: LYASE
• Organism(s): Phaeodactylum tricornutum CCAP 1055/1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-08 Released: 2021-06-16 
• Deposition Author(s): Fedorov, E., Belinski, V.A., Brunson, J.K., Almo, S.C., Dupont, C.L., Ghosh, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.241 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

The Phaeodactylum tricornutum diaminopimelate decarboxylase was acquired via horizontal gene transfer from bacteria and displays substrate promiscuity

Bielinski, V.A., Brunson, J.K., Ghosh, A., Moosburner, M.A., Garza, E.A., Fussy, Z., Bai, J., McKinnie, S.M.K., Moore, B.S., Allen, A.E., Almo, S.C., Dupont, C.L.

(2020) Biorxiv 

• DOI: https://doi.org/10.1101/2020.10.01.322594

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 94.58 kDa 
• Atom Count: 6,563 
• Modelled Residue Count: 866 
• Deposited Residue Count: 882 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A, B	441	Phaeodactylum tricornutum CCAP 1055/1	Mutation(s): 0  Gene Names: PHATRDRAFT_21592
UniProt
Find proteins for B7G3A2 (Phaeodactylum tricornutum (strain CCAP 1055/1)) Explore B7G3A2  Go to UniProtKB:  B7G3A2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DLY (Subject of Investigation/LOI)	C [auth A]	D-LYSINE C6 H14 N2 O2 KDXKERNSBIXSRK-RXMQYKEDSA-N
SO4 (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.241 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.78	α = 90
b = 86.324	β = 90
c = 127.196	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Fedorov, E., Belinski, V.A., Brunson, J.K., Almo, S.C., Dupont, C.L., Ghosh, A.

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description