6ZK8 | pdb_00006zk8

Native crystal structure of anaerobic F420H2-Oxidase from Methanothermococcus thermolithotrophicus at 1.8A resolution

PDB DOI: https://doi.org/10.2210/pdb6ZK8/pdb

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

Deposited: 2020-06-30 Released: 2020-11-25
Deposition Author(s): Engilberge, S., Wagner, T., Carpentier, P., Girard, E., Shima, S.
Funding Organization(s): French National Research Agency, Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.178 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Krypton-derivatization highlights O 2 -channeling in a four-electron reducing oxidase.

Engilberge, S., Wagner, T., Carpentier, P., Girard, E., Shima, S.

(2020) Chem Commun (Camb) 56: 10863-10866

PubMed: 32940290 Search on PubMed
DOI: https://doi.org/10.1039/d0cc04557h
Primary Citation Related Structures:
6ZK8, 6ZLF

PubMed Abstract:
F420H2-oxidase (FprA) catalyses the four-electron reduction of O2 to 2H2O using the reduced form of F420 as electron donor. The hydrophobic O2-channel detected by Kr-derivatization and the concerted movement of a gating loop could contribute to prevent unwanted side-reaction between the catalytic intermediates and solvents, therefore preventing reactive oxygen species formation.

Organizational Affiliation

Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland.

Macromolecule Content

Total Structure Weight: 95.66 kDa
Atom Count: 7,269
Modeled Residue Count: 820
Deposited Residue Count: 820
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 [auth O]	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
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain AA [auth O] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth O] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth O]	AA [auth O], J [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain AA [auth O] Focus chain J [auth A] Interactions & Density Focus chain AA [auth O] Focus chain J [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth O] SDF format, chain R [auth O] SDF format, chain G [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth O] MOL2 format, chain R [auth O] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth O] mmCIF format, chain R [auth O] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth A] H [auth A] C [auth A], D [auth A], E [auth A], G [auth A], H [auth A], Q [auth O], R [auth O]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth O] Focus chain R [auth O] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth O] Focus chain R [auth O]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain S [auth O] SDF format, chain T [auth O] SDF format, chain U [auth O] SDF format, chain V [auth O] SDF format, chain W [auth O] SDF format, chain X [auth O] SDF format, chain O [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth O] MOL2 format, chain T [auth O] MOL2 format, chain U [auth O] MOL2 format, chain V [auth O] MOL2 format, chain W [auth O] MOL2 format, chain X [auth O] MOL2 format, chain O [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain S [auth O] mmCIF format, chain T [auth O] mmCIF format, chain U [auth O] mmCIF format, chain V [auth O] mmCIF format, chain W [auth O] mmCIF format, chain X [auth O] mmCIF format, chain O [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], S [auth O], T [auth O], U [auth O], V [auth O], W [auth O], X [auth O]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth O] Focus chain T [auth O] Focus chain U [auth O] Focus chain V [auth O] Focus chain W [auth O] Focus chain X [auth O] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth O] Focus chain T [auth O] Focus chain U [auth O] Focus chain V [auth O] Focus chain W [auth O] Focus chain X [auth O]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth A] SDF format, chain Z [auth O] SDF format, chain Y [auth O] MOL2 format, chain I [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth O] MOL2 format, chain Y [auth O] mmCIF format, chain I [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth O] mmCIF format, chain Y [auth O]	I [auth A], P [auth A], Y [auth O], Z [auth O]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth A] Focus chain Y [auth O] Focus chain Z [auth O] Interactions & Density Focus chain I [auth A] Focus chain P [auth A] Focus chain Y [auth O] Focus chain Z [auth O]