6HK1

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


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 1.1 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:  
    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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiazole synthaseA, B, C, D, E, F261Methanothermococcus thermolithotrophicusMutation(s): 0 
Gene Names: thi4
EC: 2.4.2.59
UniProt
Find proteins for A0A5H1ZR31 (Methanothermococcus thermolithotrophicus)
Explore A0A5H1ZR31 
Go to UniProtKB:  A0A5H1ZR31
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
48F (Subject of Investigation/LOI)
Query on 48F

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
TB
Query on TB

Download Ideal Coordinates CCD File 
AB [auth E] , BA [auth C] , BB [auth E] , CA [auth C] , CB [auth E] , DA [auth C] , DB [auth E] , EA [auth C] , 
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
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
GB [auth E], PB [auth F], U [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
KA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
OB [auth F], T [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
FB [auth E]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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 = 216.863α = 90
b = 216.863β = 90
c = 207.25γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

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