6HF6

Crystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococcus horikoshii co-crystallized with Tb-Xo4.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Literature

Protein crystal structure determination with the crystallophore, a nucleating and phasing agent.

Engilberge, S., Wagner, T., Santoni, G., Breyton, C., Shima, S., Franzetti, B., Riobe, F., Maury, O., Girard, E.

(2019) J Appl Crystallogr 52: 722-731

  • DOI: https://doi.org/10.1107/S1600576719006381
  • Primary Citation of Related Structures:  
    6HF6, 6HF7, 6HK1

  • PubMed Abstract: 

    Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.

    • Organizational Affiliation: 

    Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deglycase PH1704
A, B, C
166Pyrococcus horikoshii OT3Mutation(s): 3 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59413
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7MT
Query on 7MT
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
K [auth C]		Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
TB
Query on TB
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
M [auth C]		TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
MLI
Query on MLI
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C]		MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.62α = 90
b = 124.62β = 90
c = 130.31γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations