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 

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Ligand Structure Quality Assessment 


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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 synthase
A, B, C, D, E, F
A, B, C, D, E, F
261Methanothermococcus thermolithotrophicusMutation(s): 0 
Gene Names: thi4
EC: 2.4.2.59
UniProt
Find proteins for A0A5H1ZR31 (Methanothermococcus thermolithotrophicus)
Explore A0A5H1ZR31 
Go to UniProtKB:  A0A5H1ZR31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5H1ZR31
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
48F
Query on 48F
Download Ideal Coordinates CCD File 
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		 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],
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
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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
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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

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Ligand Structure Quality Assessment 


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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