6LCD | pdb_00006lcd

Crystal structure of AaTPS with PPi

• PDB DOI: https://doi.org/10.2210/pdb6LCD/pdb

• Classification: LYASE
• Organism(s): Alternaria alternata
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-18 Released: 2020-07-01 
• Deposition Author(s): He, H., Mori, T., Abe, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.283 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AaTPS

He, H., Mori, T., Abe, I.

(2020) Nat Commun 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.34 kDa 
• Atom Count: 5,995 
• Modeled Residue Count: 745 
• Deposited Residue Count: 860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AaTPS	A, B	430	Alternaria alternata	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPP (Subject of Investigation/LOI)	C [auth A], G [auth B]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
MG (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.283 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.492	α = 90
b = 113.688	β = 90
c = 149.915	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): He, H., Mori, T., Abe, I.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description