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 

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:  

  • 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 co ...

    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

    Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France.,Structural Biology Group, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.,Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylate kinase
A, B, C
192Methanothermococcus thermolithotrophicusMutation(s): 0 
Gene Names: adkA (adk)
EC: 2.7.4.3
Find proteins for P43410 (Methanothermococcus thermolithotrophicus)
Go to UniProtKB:  P43410
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB

Download SDF File 
Download CCD File 
A, C
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
7MT
Query on 7MT

Download SDF File 
Download CCD File 
A, B
Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 131.326α = 90.00
b = 131.326β = 90.00
c = 88.403γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
SCALAdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Database references