8RJA

Crystal structure of the F420-reducing formylmethanofuran dehydrogenase complex from the ethanotroph Candidatus Ethanoperedens thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.210 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted MGDClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

F420 reduction as a cellular driver for anaerobic ethanotrophy

Lemaire, O.N.Wegener, G.Wagner, T.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase subunit A
A, G
567Candidatus Methanoperedenaceae archaeon GB50Mutation(s): 0 
EC: 3.5.2.5
UniProt
Find proteins for A0A7R9MYH2 (Candidatus Methanoperedenaceae archaeon GB50)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9MYH2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase subunit B
B, H
430Candidatus Methanoperedenaceae archaeon GB50Mutation(s): 0 
UniProt
Find proteins for A0A7R9R4U5 (Candidatus Methanoperedenaceae archaeon GB50)
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UniProt GroupA0A7R9R4U5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
formylmethanofuran dehydrogenase
C, I
253Candidatus Methanoperedenaceae archaeon GB50Mutation(s): 0 
EC: 1.2.7.12
UniProt
Find proteins for A0A7R9MYM1 (Candidatus Methanoperedenaceae archaeon GB50)
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UniProt GroupA0A7R9MYM1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase subunit D
D, J
126Candidatus Methanoperedenaceae archaeon GB50Mutation(s): 0 
EC: 1.2.7.12
UniProt
Find proteins for A0A7R9R4V6 (Candidatus Methanoperedenaceae archaeon GB50)
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UniProt GroupA0A7R9R4V6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
E, K
359Candidatus Methanoperedenaceae archaeon GB50Mutation(s): 0 
UniProt
Find proteins for A0A7R9N9K9 (Candidatus Methanoperedenaceae archaeon GB50)
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UniProt GroupA0A7R9N9K9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
F, L
85Candidatus Methanoperedenaceae archaeon GB50Mutation(s): 0 
EC: 1.6.5.11
UniProt
Find proteins for A0A7R9MZV2 (Candidatus Methanoperedenaceae archaeon GB50)
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UniProt GroupA0A7R9MZV2
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  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
JA [auth E],
TB [auth K]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MGD (Subject of Investigation/LOI)
Query on MGD

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AA [auth B],
BA [auth B],
DB [auth H],
EB [auth H]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
PE4
Query on PE4

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EA [auth B],
PB [auth I],
R [auth A]
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
BB [auth H]
HA [auth E]
IA [auth E]
KA [auth E]
RA [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
PG4
Query on PG4

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NB [auth I]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
W (Subject of Investigation/LOI)
Query on W

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CB [auth H],
Z [auth B]
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
PEG
Query on PEG

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

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FB [auth H]
IB [auth H]
JB [auth H]
LA [auth E]
MB [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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M [auth A],
N [auth A],
UA [auth G],
VA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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AB [auth G]
FA [auth B]
KB [auth H]
MA [auth E]
NA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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DA [auth B],
HB [auth H],
Q [auth A],
QB [auth I],
S [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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AC [auth L],
GA [auth C],
TA [auth F],
X [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
CA [auth B],
GB [auth H]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
LB [auth H],
QA [auth E],
WA [auth G],
XB [auth K]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, G
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.210 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.627α = 90
b = 135.636β = 90.49
c = 149.902γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted MGDClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyWA 4053/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release