6F2H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1002/chem.201802172
  • Primary Citation of Related Structures:  

  • 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 systematic ...

    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.,Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 518, F-69342, Lyon, France.,Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deglycase PH1704
A, B, C, D, E, F, G, H, I, J, K, L
166Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
EC: 3.5.1.124
Find proteins for O59413 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O59413
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB

Download SDF File 
Download CCD File 
C, D, E, F, H, J, K
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, C, E, F, G, H, I, J, K, L
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
7MT
Query on 7MT

Download SDF File 
Download CCD File 
A, B, E, F, G, I, J, K, L
Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.577α = 90.00
b = 84.698β = 90.97
c = 144.343γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
SCALAdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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