6TH5 | pdb_00006th5

Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975

• PDB DOI: https://doi.org/10.2210/pdb6TH5/pdb

• Classification: TRANSFERASE
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-18 Released: 2020-11-25 
• Deposition Author(s): Feiler, C.G., Blankenfeldt, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975

Feiler, C.G., Blankenfeldt, W.

To be published.

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: 49.49 kDa 
• Atom Count: 3,724 
• Modeled Residue Count: 427 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alr0975 protein	A, B	218	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: alr0975 EC: 2.3.2.15
UniProt
Find proteins for Q8YY76 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YY76  Go to UniProtKB:  Q8YY76

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.356	α = 90
b = 46.67	β = 92.258
c = 68.583	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Feiler, C.G., Blankenfeldt, W.

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description