6FRN | pdb_00006frn

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

PDB DOI: https://doi.org/10.2210/pdb6FRN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanothermococcus thermolithotrophicus
Mutation(s): No

Deposited: 2018-02-16 Released: 2018-10-03
Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Wagner, T., Shima, S., Girard, E., Dumont, E., Maury, O.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.189 (Depositor), 0.192 (DCC)
R-Value Work:
0.164 (Depositor), 0.167 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 29806881 Search on PubMed
DOI: https://doi.org/10.1002/chem.201802172
Primary Citation Related Structures:
6F2F, 6F2H, 6F2I, 6F2J, 6F2K, 6F2M, 6FRM, 6FRN, 6FRO, 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). 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

Univ Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.

Macromolecule Content

Total Structure Weight: 192.96 kDa
Atom Count: 14,150
Modeled Residue Count: 1,624
Deposited Residue Count: 1,640
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F420H2 oxidase (FprA)	A, B, C, D	410	Methanothermococcus thermolithotrophicus	Mutation(s): 0
UniProt
Find proteins for A0A452CSW8 (Methanothermococcus thermolithotrophicus) Explore A0A452CSW8 Go to UniProtKB: A0A452CSW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A452CSW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MT Query on 7MT Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain MA [auth D] SDF format, chain LA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D]	LA [auth D], MA [auth D], Y [auth C], Z [auth C]	Tb-Xo4 C₂₀ H₂₃ N₅ O₄ Tb JWLMJALAUZUFRC-UHFFFAOYSA-L		Interactions Focus chain LA [auth D] Focus chain MA [auth D] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain LA [auth D] Focus chain MA [auth D] Focus chain Y [auth C] Focus chain Z [auth C]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain K [auth B] SDF format, chain EA [auth D] SDF format, chain E [auth A] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain E [auth A] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain E [auth A]	E [auth A], EA [auth D], K [auth B], R [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth D] Focus chain K [auth B] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth D] Focus chain K [auth B] Focus chain R [auth C]
PE4 Query on PE4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain OA [auth D] SDF format, chain O [auth B] SDF format, chain NA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] NA [auth D] O [auth B] OA [auth D] 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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B]
TB Query on TB Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain N [auth B] SDF format, chain KA [auth D] SDF format, chain I [auth A] MOL2 format, chain X [auth C] MOL2 format, chain N [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain I [auth A] mmCIF format, chain X [auth C] mmCIF format, chain N [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain I [auth A]	I [auth A], KA [auth D], N [auth B], X [auth C]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain KA [auth D] Focus chain N [auth B] Focus chain X [auth C] Interactions & Density Focus chain I [auth A] Focus chain KA [auth D] Focus chain N [auth B] Focus chain X [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain QA [auth D] SDF format, chain Q [auth B] SDF format, chain PA [auth D] SDF format, chain J [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C]	CA [auth C] DA [auth C] J [auth A] PA [auth D] Q [auth B] 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		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain J [auth A] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain J [auth A] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain JA [auth D] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A]	F [auth A] FA [auth D] G [auth A] GA [auth D] H [auth A] 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		Interactions Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain RA [auth D] MOL2 format, chain RA [auth D] mmCIF format, chain RA [auth D]	RA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain RA [auth D] Interactions & Density Focus chain RA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.189 (Depositor), 0.192 (DCC)
R-Value Work: 0.164 (Depositor), 0.167 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.66	α = 90
b = 144.97	β = 91.78
c = 74.21	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-03

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-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
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations