3OR1 | pdb_00003or1

Crystal structure of dissimilatory sulfite reductase I (DsrI)

• PDB DOI: https://doi.org/10.2210/pdb3OR1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Megalodesulfovibrio gigas
• Mutation(s): No 


• Deposited: 2010-09-06 Released: 2010-09-22 
• Deposition Author(s): Hsieh, Y.C., Liu, M.Y., Wang, V.C.C., Chiang, Y.L., Liu, E.H., Wu, W.G., Chan, S.I., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.212 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Structure insights into the enzyme catalysis from comparison of three forms of dissimilatory sulfite reductase from Desulfovibrio gigas

Hsieh, Y.C., Liu, M.Y., Wang, V.C.C., Chiang, Y.L., Liu, E.H., Wu, W.G., Chan, S.I., Chen, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Macromolecule Content 

• Total Structure Weight: 213.11 kDa 
• Atom Count: 15,467 
• Modeled Residue Count: 1,848 
• Deposited Residue Count: 1,856 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfite reductase alpha	A, D	437	Megalodesulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for E2QR97 (Megalodesulfovibrio gigas) Explore E2QR97  Go to UniProtKB:  E2QR97

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfite reductase beta	B, E	386	Megalodesulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for E2QR96 (Megalodesulfovibrio gigas) Explore E2QR96  Go to UniProtKB:  E2QR96

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfite reductase gama	C, F	105	Megalodesulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for E2QR98 (Megalodesulfovibrio gigas) Explore E2QR98  Go to UniProtKB:  E2QR98

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRM	H [auth A], K [auth B], O [auth D], R [auth E]	SIROHEME C42 H44 Fe N4 O16 DLKSSIHHLYNIKN-MWBYXLBFSA-L
SF4	I [auth A], J [auth A], L [auth B], M [auth B], P [auth D], Q [auth D], S [auth E], T [auth E]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SO3	G [auth A], N [auth D]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.212 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.721	α = 90
b = 60.478	β = 94.3
c = 132.915	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Hsieh, Y.C., Liu, M.Y., Wang, V.C.C., Chiang, Y.L., Liu, E.H., Wu, W.G., Chan, S.I., Chen, C.J.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-10-30
  Changes: Structure summary