6FRN

Structure of F420H2 oxidase (FprA) co-crystallized with 10mM Tb-Xo4 and calcium chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.

Engilberge, S.Riobe, F.Wagner, T.Di Pietro, S.Breyton, C.Franzetti, B.Shima, S.Girard, E.Dumont, E.Maury, O.

(2018) Chemistry 24: 9739-9746

  • DOI: 10.1002/chem.201802172
  • Primary Citation of Related Structures:  
    6F2K, 6F2J, 6F2M, 6F2F, 6F2I, 6F2H, 6FRM, 6FRO, 6FRN, 6FRQ

  • PubMed Abstract: 
  • Crystallophores are lanthanide complexes that act as powerful auxiliary for protein crystallography due to their strong nucleating and phasing effects. To get first insights on the mechanisms behind nucleation induced by Crystallophore, we systematically identified various elaborated networks of supramolecular interactions between Tb-Xo4 and subset of 6 protein structures determined by X-ray diffraction in complex with terbium-Crystallophore (Tb-Xo4) ...

    Crystallophores are lanthanide complexes that act as powerful auxiliary for protein crystallography due to their strong nucleating and phasing effects. To get first insights on the mechanisms behind nucleation induced by Crystallophore, we systematically identified various elaborated networks of supramolecular interactions between Tb-Xo4 and subset of 6 protein structures determined by X-ray diffraction in complex with terbium-Crystallophore (Tb-Xo4). Such interaction mapping analyses demonstrate the versatile binding behavior of the Crystallophore and pave the way to a better understanding of its unique properties.


    Organizational Affiliation

    Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 518, F-69342, Lyon, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F420H2 oxidase (FprA)A, B, C, D410Methanothermococcus thermolithotrophicusMutation(s): 0 
UniProt
Find proteins for A0A452CSW8 (Methanothermococcus thermolithotrophicus)
Explore A0A452CSW8 
Go to UniProtKB:  A0A452CSW8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MT (Subject of Investigation/LOI)
Query on 7MT

Download Ideal Coordinates CCD File 
LA [auth D], MA [auth D], Y [auth C], Z [auth C]Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
E [auth A], EA [auth D], K [auth B], R [auth C]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
PE4
Query on PE4

Download Ideal Coordinates CCD File 
AA [auth C], BA [auth C], NA [auth D], O [auth B], OA [auth D], P [auth B]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
TB
Query on TB

Download Ideal Coordinates CCD File 
I [auth A], KA [auth D], N [auth B], X [auth C]TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth C], DA [auth C], J [auth A], PA [auth D], Q [auth B], QA [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A] , FA [auth D] , G [auth A] , GA [auth D] , H [auth A] , HA [auth D] , IA [auth D] , JA [auth D] , 
F [auth A],  FA [auth D],  G [auth A],  GA [auth D],  H [auth A],  HA [auth D],  IA [auth D],  JA [auth D],  L [auth B],  M [auth B],  S [auth C],  T [auth C],  U [auth C],  V [auth C],  W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
RA [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.66α = 90
b = 144.97β = 91.78
c = 74.21γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Derived calculations, Structure summary