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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.219 (Depositor), 0.190 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 212.42 kDa
Atom Count: 15,433
Modelled Residue Count: 1,848
Deposited Residue Count: 1,848
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E2QR97
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E2QR96
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E2QR99
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRM Query on SRM Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain T [auth E] SDF format, chain R [auth D] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D]	J [auth A], L [auth B], R [auth D], T [auth E]	SIROHEME C₄₂ H₄₄ Fe N₄ O₁₆ DLKSSIHHLYNIKN-MWBYXLBFSA-L		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain R [auth D] Focus chain T [auth E] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain R [auth D] Focus chain T [auth E]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain M [auth B]	G [auth A] H [auth A] M [auth B] N [auth B] O [auth D] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain U [auth E] Focus chain V [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain U [auth E] Focus chain V [auth E]
SO3 Query on SO3 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth D] SDF format, chain S [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D]	I [auth A], K [auth A], Q [auth D], S [auth D]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain Q [auth D] Focus chain S [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain Q [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.219 (Depositor), 0.190 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Revision History (Full details and data files)

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

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Deposit Data

Help and Resources

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Crystal structure of dissimilatory sulfite reductase II (DsrII)

Dissimilatory Sulfite Reductase, Sulfate Reduction

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3OR2 | pdb_00003or2