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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiazole synthase
A, B, C, D, E
A, B, C, D, E, F
261Methanothermococcus thermolithotrophicusMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / 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
TB
Query on TB

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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
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
PEG
Query on PEG

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KA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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OB [auth F],
T [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

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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 = 216.863α = 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 


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