1FDI

OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED WITH THE INHIBITOR NITRITE

• PDB DOI: https://doi.org/10.2210/pdb1FDI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-01-28 Released: 1997-08-20 
• Deposition Author(s): Sun, P.D., Boyington, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.284 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster.

Boyington, J.C., Gladyshev, V.N., Khangulov, S.V., Stadtman, T.C., Sun, P.D.

(1997) Science 275: 1305-1308

• PubMed: 9036855 
• DOI: https://doi.org/10.1126/science.275.5304.1305
• Primary Citation of Related Structures:  
  1AA6, 1FDI, 1FDO


• PubMed Abstract: 
  

  Formate dehydrogenase H from Escherichia coli contains selenocysteine (SeCys), molybdenum, two molybdopterin guanine dinucleotide (MGD) cofactors, and an Fe4S4 cluster at the active site and catalyzes the two-electron oxidation of formate to carbon dioxide. The crystal structures of the oxidized [Mo(VI), Fe4S4(ox)] form of formate dehydrogenase H (with and without bound inhibitor) and the reduced [Mo(IV), Fe4S4(red)] form have been determined, revealing a four-domain alphabeta structure with the molybdenum directly coordinated to selenium and both MGD cofactors. These structures suggest a reaction mechanism that directly involves SeCys140 and His141 in proton abstraction and the molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron transfer.

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Organizational Affiliation: 

Laboratory of Molecular Structure, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD 20852, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.44 kDa 
• Atom Count: 5,743 
• Modelled Residue Count: 715 
• Deposited Residue Count: 715 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE DEHYDROGENASE H	A	715	Escherichia coli	Mutation(s): 0  Gene Names: FDHF EC: 1.2.1.2 (PDB Primary Data), 1.17.98.4 (UniProt)
UniProt
Find proteins for P07658 (Escherichia coli (strain K12)) Explore P07658  Go to UniProtKB:  P07658

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGD	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
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
6MO	F [auth A]	MOLYBDENUM(VI) ION Mo HCNGUXXTNNIKCQ-UHFFFAOYSA-N
NO2	B [auth A]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.284 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.8	α = 90
b = 146.8	β = 90
c = 81.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-08-20 
Deposition Author(s): Sun, P.D., Boyington, J.C.

Revision History  

• Version 1.0: 1997-08-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-01-29
  Changes: Structure summary
• Version 1.4: 2014-08-06
  Changes: Derived calculations, Structure summary
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other