Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 179.44 kDa 
• Atom Count: 12396 
• Modelled Residue Count: 1556 
• Deposited Residue Count: 1566 
• Unique protein chains: 1

6HK1

Crystal structure of the Thiazole synthase from Methanothermococcus thermolithotrophicus co-crystallized with Tb-Xo4

• DOI: 10.2210/pdb6HK1/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Methanothermococcus thermolithotrophicus
• Mutation(s): No 


• Deposited: 2018-09-05 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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.213 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

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: 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiazole synthase	A, B, C, D, E, F	261	Methanothermococcus thermolithotrophicus	Mutation(s): 0  Gene Names: thi4 EC: 2.4.2.59
UniProt
Find proteins for A0A5H1ZR31 (Methanothermococcus thermolithotrophicus) Explore A0A5H1ZR31  Go to UniProtKB:  A0A5H1ZR31

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
48F (Subject of Investigation/LOI)	AA [auth B], EB [auth E], JA [auth C], NB [auth F], S [auth A], SA [auth D]	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate C15 H23 N5 O14 P2 HMVGRTYSZXZGQZ-GHVQHMAVSA-N
TB	AB [auth E], BA [auth C], BB [auth E], CA [auth C], CB [auth E], DA [auth C], DB [auth E], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], HB [auth F], I [auth A], IA [auth C], IB [auth F], J [auth A], JB [auth F], K [auth A], KB [auth F], L [auth A], LA [auth D], LB [auth F], M [auth A], MA [auth D], MB [auth F], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], TA [auth E], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], XA [auth E], Y [auth B], YA [auth E], Z [auth B], ZA [auth E]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
PGE	GB [auth E], PB [auth F], U [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	KA [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	OB [auth F], T [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	FB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.213 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.863	α = 90
b = 216.863	β = 90
c = 207.25	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-09-05 
• 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.

---

Funding Organization	Location	Grant Number
French National Research Agency	France	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