6F2F

Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate.

• PDB DOI: https://doi.org/10.2210/pdb6F2F/pdb

• Classification: CELL CYCLE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-24 Released: 2018-10-03 
• Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Franzetti, B., Girard, E., Dumont, E., Maury, O.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.

Engilberge, S., Riobe, F., Wagner, T., Di Pietro, S., Breyton, C., Franzetti, B., Shima, S., Girard, E., Dumont, E., Maury, O.

(2018) Chemistry 24: 9739-9746

• PubMed: 29806881 
• DOI: https://doi.org/10.1002/chem.201802172
• Primary Citation of Related Structures:  
  6F2F, 6F2H, 6F2I, 6F2J, 6F2K, 6F2M, 6FRM, 6FRN, 6FRO, 6FRQ


• PubMed Abstract: 
  

  Crystallophores are lanthanide complexes that act as powerful auxiliary for protein crystallography due to their strong nucleating and phasing effects. To get first insights on the mechanisms behind nucleation induced by Crystallophore, we systematically identified various elaborated networks of supramolecular interactions between Tb-Xo4 and subset of 6 protein structures determined by X-ray diffraction in complex with terbium-Crystallophore (Tb-Xo4). Such interaction mapping analyses demonstrate the versatile binding behavior of the Crystallophore and pave the way to a better understanding of its unique properties.

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Organizational Affiliation: 

Univ Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.64 kDa 
• Atom Count: 4,731 
• Modelled Residue Count: 498 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deglycase PH1704	A, B, C	166	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH1704 EC: 3.5.1.124 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for O59413 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59413  Go to UniProtKB:  O59413

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7MT	D [auth A], H [auth B], L [auth C]	Tb-Xo4 C20 H23 N5 O4 Tb JWLMJALAUZUFRC-UHFFFAOYSA-L
TB	G [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
2HA	P [auth C]	Dihydroxyacetone C3 H6 O3 RXKJFZQQPQGTFL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.588	α = 90
b = 124.588	β = 90
c = 128.866	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Franzetti, B., Girard, E., Dumont, E., Maury, O.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-13-BS07-0007-01

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2020-07-08
  Changes: Derived calculations, Structure summary
• Version 1.4: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description