7XQW

Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)

PDB DOI: https://doi.org/10.2210/pdb7XQW/pdb
EM Map EMD-33402: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Methylorubrum extorquens AM1
Expression System: Methylorubrum extorquens AM1
Mutation(s): No

Deposited: 2022-05-09 Released: 2023-08-09
Deposition Author(s): Park, J., Heo, Y.Y., Roh, S.H., Lee, H.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Enzymatic conversion of CO2 in real flue gas to molar-scale formate

Jeon, B.W., Heo, Y.Y., Park, J., Roh, S.H., Lee, H.H., Kim, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 174.57 kDa
Atom Count: 10,391
Modelled Residue Count: 1,331
Deposited Residue Count: 1,567
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A	995	Methylorubrum extorquens AM1	Mutation(s): 0 Gene Names: fdh1A, MexAM1_META1p5032 EC: 1.17.1.9
UniProt
Find proteins for C5ATT7 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5ATT7 Go to UniProtKB: C5ATT7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5ATT7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten-containing formate dehydrogenase beta subunit	B	572	Methylorubrum extorquens AM1	Mutation(s): 0 Gene Names: fdh1B, MexAM1_META1p5031 EC: 1.2.1.2
UniProt
Find proteins for C5ATT6 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5ATT6 Go to UniProtKB: C5ATT6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5ATT6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD (Subject of Investigation/LOI) Query on MGD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B]	G [auth A], H [auth A], I [auth A], K [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B]
W Query on W Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B]	F [auth A], L [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021M3A9I4021220
National Research Foundation (NRF, Korea)	Korea, Republic Of	2019M3E5D6063871

Revision History (Full details and data files)

Version 1.0: 2023-08-09
Type: Initial release

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Help and Resources

7XQW

Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1)

Enzymatic conversion of CO2 in real flue gas to molar-scale formate

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2