Structure of Protease 1 from Pyrococcus horikoshii co-crystallized in presence of 10 mM Tb-Xo4 and potassium iodide.

Experimental Data Snapshot

  • Resolution: 2.19 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report

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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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deglycase PH1704
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
166Pyrococcus horikoshiiMutation(s): 0 
Gene Names: PH1704
EC: (PDB Primary Data), 3.4.22 (PDB Primary Data)
Find proteins for O59413 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59413 
Go to UniProtKB:  O59413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59413
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 7MT

Download Ideal Coordinates CCD File 
BA [auth G]
FA [auth I]
IA [auth J]
LA [auth K]
M [auth A]
BA [auth G],
FA [auth I],
IA [auth J],
LA [auth K],
M [auth A],
NA [auth L],
O [auth B],
V [auth E],
Z [auth F]
C20 H23 N5 O4 Tb
Query on TB

Download Ideal Coordinates CCD File 
DA [auth H]
HA [auth J]
KA [auth K]
Q [auth C]
S [auth D]
DA [auth H],
HA [auth J],
KA [auth K],
Q [auth C],
S [auth D],
T [auth E],
U [auth E],
X [auth F],
Y [auth F]
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
JA [auth J]
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
JA [auth J],
MA [auth K],
N [auth A],
OA [auth L],
P [auth B],
R [auth C],
W [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.19 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.577α = 90
b = 84.698β = 90.97
c = 144.343γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-BS07-0007-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Derived calculations, Structure summary