3OR2 | pdb_00003or2

Crystal structure of dissimilatory sulfite reductase II (DsrII)

• PDB DOI: https://doi.org/10.2210/pdb3OR2/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: 2.05 Å
• R-Value Free: 
  0.219 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Dissimilatory Sulfite Reductase, Sulfate Reduction

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: 212.42 kDa 
• Atom Count: 15,433 
• Modeled Residue Count: 1,848 
• Deposited Residue Count: 1,848 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfite redcutase subunit alpha	A, D	435	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 redcutase subunit beta	B, E	385	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 redcutase subunit gama	C, F	104	Megalodesulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for E2QR99 (Megalodesulfovibrio gigas) Explore E2QR99  Go to UniProtKB:  E2QR99

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.219 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.129	α = 90
b = 59.977	β = 94.24
c = 133.208	γ = 90

Software Package:

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

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 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-12-27
  Changes: Data collection, Non-polymer description, Structure summary
• Version 2.1: 2024-10-30
  Changes: Structure summary