3FO3 | pdb_00003fo3

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)

• PDB DOI: https://doi.org/10.2210/pdb3FO3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thioalkalivibrio nitratireducens
• Mutation(s): No 


• Deposited: 2008-12-27 Released: 2009-12-29 
• Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.139 (Depositor), 0.141 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

Literature

Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide

Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Tikhonova, T.V., Safonova, T.N., Tikhonov, A.V., Popov, A.N., Popov, V.O.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1043-1047

• PubMed: 20944237 
• DOI: https://doi.org/10.1107/S0907444910031665
• Primary Citation Related Structures: 
  3FO3, 3MMO


• PubMed Abstract: 
  

  The structures of complexes of octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR) with the substrate sulfite (1.4 Å resolution; R(cryst) = 0.126) and the inhibitor cyanide (1.55 Å resolution; R(cryst) = 0.148) have been established. The complex with sulfite was prepared by the reduction of the protein crystal with sodium dithionite. The sulfite ion is bound to the iron ion of the catalytic haem through the S atom. The Fe-S distance is 2.24 Å. The structure of the cyanide complex with full occupancy of the ligand site was established for the first time for cytochrome c nitrite reductases. The cyanide ion is bound to the catalytic haem iron through the C atom. The Fe-C distance is 1.91 Å and the Fe-C-N angle is 171°. The sulfite reductase activity of TvNiR was measured at different pH values. The activity is 0.02 µmol of HS(-) per minute per milligram at pH 7.0; it decreases with increasing pH and is absent at pH 9.0.

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Organizational Affiliation: 
• Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.35 kDa 
• Atom Count: 10,671 
• Modeled Residue Count: 1,038 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eight-heme nitrite reductase	A, B	525	Thioalkalivibrio nitratireducens	Mutation(s): 0  EC: 1.7.2.2
UniProt
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2)) Explore L0DSL2  Go to UniProtKB:  L0DSL2

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], KA [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
PG6	AA [auth A], BA [auth A], BB [auth B], Q [auth A], RA [auth B], S [auth A], U [auth A], UA [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4	AB [auth B], CB [auth B], DB [auth B], EB [auth B], GB [auth B], T [auth A], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS	R [auth A], SA [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
THJ	O [auth A], PA [auth B]	THIOSULFATE O3 S2 DHCDFWKWKRSZHF-UHFFFAOYSA-L
SO4	N [auth A], TA [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
SO3	K [auth A], LA [auth B], OA [auth B]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L
ACT	FB [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	L [auth A], M [auth A], MA [auth B], NA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	CA [auth A], HB [auth B], IB [auth B], P [auth A], QA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.139 (Depositor), 0.141 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.79	α = 90
b = 193.79	β = 90
c = 193.79	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary