6HF7

Crystal structure of the adenylate kinase from Methanothermococcus thermolithotrophicus co-crystallized with Tb-Xo4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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: 10.1107/S1600576719006381
  • Primary Citation of Related Structures:  
    6HF7, 6HF6, 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenylate kinaseA, B, C192Methanothermococcus thermolithotrophicusMutation(s): 0 
Gene Names: adkAadk
EC: 2.7.4.3
UniProt
Find proteins for P43410 (Methanothermococcus thermolithotrophicus)
Explore P43410 
Go to UniProtKB:  P43410
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.326α = 90
b = 131.326β = 90
c = 88.403γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceLn23 ANR-13-BS07-0007-01
Max Planck SocietyGermany--

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