6HK1

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

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 31396026 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 179.44 kDa
Atom Count: 12,396
Modelled Residue Count: 1,556
Deposited Residue Count: 1,566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiazole synthase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5H1ZR31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
48F Query on 48F Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain EB [auth E] SDF format, chain JA [auth C] SDF format, chain NB [auth F] SDF format, chain S [auth A] SDF format, chain SA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain EB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain NB [auth F] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth D]	AA [auth B] EB [auth E] JA [auth C] NB [auth F] S [auth A] 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		Interactions Focus chain AA [auth B] Focus chain EB [auth E] Focus chain JA [auth C] Focus chain NB [auth F] Focus chain S [auth A] Focus chain SA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain EB [auth E] Focus chain JA [auth C] Focus chain NB [auth F] Focus chain S [auth A] Focus chain SA [auth D]
TB Query on TB Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BA [auth C] SDF format, chain BB [auth E] SDF format, chain CA [auth C] SDF format, chain CB [auth E] SDF format, chain DA [auth C] SDF format, chain DB [auth E] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth F] SDF format, chain J [auth A] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth E] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth E]	AB [auth E] BA [auth C] BB [auth E] CA [auth C] CB [auth E] 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		Interactions Focus chain AB [auth E] Focus chain BA [auth C] Focus chain BB [auth E] Focus chain CA [auth C] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BA [auth C] Focus chain BB [auth E] Focus chain CA [auth C] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth F] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain GB [auth E] SDF format, chain PB [auth F] SDF format, chain U [auth A] MOL2 format, chain GB [auth E] MOL2 format, chain PB [auth F] MOL2 format, chain U [auth A] mmCIF format, chain GB [auth E] mmCIF format, chain PB [auth F] mmCIF format, chain U [auth A]	GB [auth E], PB [auth F], U [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain GB [auth E] Focus chain PB [auth F] Focus chain U [auth A] Interactions & Density Focus chain GB [auth E] Focus chain PB [auth F] Focus chain U [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain KA [auth C] MOL2 format, chain KA [auth C] mmCIF format, chain KA [auth C]	KA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain KA [auth C] Interactions & Density Focus chain KA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain OB [auth F] SDF format, chain T [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain T [auth A] mmCIF format, chain OB [auth F] mmCIF format, chain T [auth A]	OB [auth F], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain OB [auth F] Focus chain T [auth A] Interactions & Density Focus chain OB [auth F] Focus chain T [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain FB [auth E] MOL2 format, chain FB [auth E] mmCIF format, chain FB [auth E]	FB [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FB [auth E] Interactions & Density Focus chain FB [auth E]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

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

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