6HF7

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

• PDB DOI:  https://doi.org/10.2210/pdb6HF7/pdb

• Classification: TRANSFERASE
• Organism(s): Methanothermococcus thermolithotrophicus
• Mutation(s): No 


• Deposited: 2018-08-21 Released: 2019-06-19 
• Deposition Author(s): Engilberge, S., Wagner, T., Santoni, G., Breyton, C., Shima, S., Franzetti, B., Riobe, F., Maury, O., Girard, E.
• Funding Organization(s): French National Research Agency, Max Planck Society

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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 

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

• PubMed: 31396026 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 66.12 kDa 
• Atom Count: 5,111 
• Modelled Residue Count: 573 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B, C	192	Methanothermococcus thermolithotrophicus	Mutation(s): 0  Gene Names: adkA, adk EC: 2.7.4.3
UniProt
Find proteins for P43410 (Methanothermococcus thermolithotrophicus) Explore P43410  Go to UniProtKB:  P43410

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7MT	D [auth A], H [auth B]	Tb-Xo4 C20 H23 N5 O4 Tb JWLMJALAUZUFRC-UHFFFAOYSA-L
TB	E [auth A], K [auth C]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
GOL	G [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 131.326	α = 90
b = 131.326	β = 90
c = 88.403	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Engilberge, S., Wagner, T., Santoni, G., Breyton, C., Shima, S., Franzetti, B., Riobe, F., Maury, O., Girard, E.

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Funding Organization	Location	Grant Number
French National Research Agency	France	Ln23 ANR-13-BS07-0007-01
Max Planck Society	Germany	--

Revision History  

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