7R66 | pdb_00007r66

Structure of Pfp1 protease from Thermococcus thioreducens: large unit cell at 1.44 A resolution

• PDB DOI: https://doi.org/10.2210/pdb7R66/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus thioreducens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-22 Released: 2021-09-29 
• Deposition Author(s): McPherson, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Structure of the Pfp1 protease from a hypothermophilic archer, Thermococcus thioreducens, in two crystal forms

Larson, S.B., McPherson, A.

(2017) Acta Crystallogr D73: 749-756

• DOI: https://doi.org/10.1107/S2059798317010622

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 74.51 kDa 
• Atom Count: 6,034 
• Modeled Residue Count: 664 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase	A, B, C, D	166	Thermococcus thioreducens	Mutation(s): 0  Gene Names: AMR53_10535
UniProt
Find proteins for A0A0Q2XKL6 (Thermococcus thioreducens) Explore A0A0Q2XKL6  Go to UniProtKB:  A0A0Q2XKL6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A], F [auth A], G [auth B], I [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	H [auth C], J [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.03	α = 90
b = 151.03	β = 90
c = 80.716	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): McPherson, A.

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection