6FRM | pdb_00006frm

Crystal Structure of coenzyme F420H2 oxidase (FprA) co-crystallized with 10 mM Tb-Xo4

PDB DOI: https://doi.org/10.2210/pdb6FRM/pdb

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

Deposited: 2018-02-16 Released: 2018-10-31
Deposition Author(s): Engilberge, S., Riobe, F., Wagner, T., Di Pietro, S., Shima, S., Girard, E., Dumont, E., Maury, O.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.209 (Depositor), 0.211 (DCC)
R-Value Work:
0.177 (Depositor), 0.179 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 377.75 kDa
Atom Count: 27,500
Modeled Residue Count: 3,222
Deposited Residue Count: 3,280
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420H2 oxidase (FprA)	A, B, C, D, E A, B, C, D, E, F, G, H	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MT Query on 7MT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F]	J [auth A], JA [auth F]	Tb-Xo4 C₂₀ H₂₃ N₅ O₄ Tb JWLMJALAUZUFRC-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain JA [auth F] Interactions & Density Focus chain J [auth A] Focus chain JA [auth F]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain KA [auth F] SDF format, chain N [auth B] SDF format, chain PA [auth G] SDF format, chain R [auth C] SDF format, chain VA [auth H] SDF format, chain X [auth D] SDF format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain R [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain X [auth D] MOL2 format, chain EA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain R [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain X [auth D] mmCIF format, chain EA [auth E]	EA [auth E] I [auth A] KA [auth F] N [auth B] PA [auth G] EA [auth E], I [auth A], KA [auth F], N [auth B], PA [auth G], R [auth C], VA [auth H], X [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain EA [auth E] Focus chain I [auth A] Focus chain KA [auth F] Focus chain N [auth B] Focus chain PA [auth G] Focus chain R [auth C] Focus chain VA [auth H] Focus chain X [auth D] Interactions & Density Focus chain EA [auth E] Focus chain I [auth A] Focus chain KA [auth F] Focus chain N [auth B] Focus chain PA [auth G] Focus chain R [auth C] Focus chain VA [auth H] Focus chain X [auth D]
TB Query on TB Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain LA [auth F] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain SA [auth G] SDF format, chain T [auth C] SDF format, chain XA [auth H] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain WA [auth H] SDF format, chain RA [auth G] SDF format, chain QA [auth G] SDF format, chain K [auth A] SDF format, chain FA [auth E] MOL2 format, chain AA [auth D] MOL2 format, chain LA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain WA [auth H] MOL2 format, chain RA [auth G] MOL2 format, chain QA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth E] mmCIF format, chain AA [auth D] mmCIF format, chain LA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain T [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain WA [auth H] mmCIF format, chain RA [auth G] mmCIF format, chain QA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth E]	AA [auth D] FA [auth E] K [auth A] LA [auth F] O [auth B] AA [auth D], FA [auth E], K [auth A], LA [auth F], O [auth B], QA [auth G], RA [auth G], S [auth C], SA [auth G], T [auth C], WA [auth H], XA [auth H], Y [auth D], Z [auth D]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain O [auth B] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain S [auth C] Focus chain SA [auth G] Focus chain T [auth C] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain O [auth B] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain S [auth C] Focus chain SA [auth G] Focus chain T [auth C] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain Y [auth D] Focus chain Z [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain TA [auth G] SDF format, chain U [auth C] SDF format, chain YA [auth H] SDF format, chain BA [auth D] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain BA [auth D] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain BA [auth D]	BA [auth D], TA [auth G], U [auth C], YA [auth H]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain TA [auth G] Focus chain U [auth C] Focus chain YA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain TA [auth G] Focus chain U [auth C] Focus chain YA [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain UA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain ZA [auth H] MOL2 format, chain AB [auth H] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain ZA [auth H] mmCIF format, chain AB [auth H] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain ZA [auth H]	AB [auth H] CA [auth D] DA [auth D] GA [auth E] HA [auth E] AB [auth H], CA [auth D], DA [auth D], GA [auth E], HA [auth E], IA [auth E], L [auth A], M [auth A], MA [auth F], NA [auth F], OA [auth F], P [auth B], Q [auth B], UA [auth G], V [auth C], W [auth C], ZA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth H] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AB [auth H] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain ZA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.209 (Depositor), 0.211 (DCC)
R-Value Work: 0.177 (Depositor), 0.179 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.17	α = 90
b = 147.875	β = 90.4
c = 146.059	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-31

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: 2018-10-31
Type: Initial release
Version 1.1: 2019-03-06
Changes: Data collection, Structure summary
Version 1.2: 2019-05-29
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description