6HK1 | pdb_00006hk1

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

• PDB DOI: https://doi.org/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.213 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

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 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.
Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
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.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
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  

Global Symmetry: Dihedral - D4  (Explore in 3D)
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: 12,396 
• Modeled Residue Count: 1,556 
• Deposited Residue Count: 1,566 
• Unique protein chains: 1

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  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	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 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

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

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	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
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Derived calculations