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- PDB-3or2: Crystal structure of dissimilatory sulfite reductase II (DsrII) -

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Basic information

Entry
Database: PDB / ID: 3or2
TitleCrystal structure of dissimilatory sulfite reductase II (DsrII)
Components(Sulfite redcutase subunit ...) x 3
KeywordsOXIDOREDUCTASE / DISSIMILATORY SULFITE REDUCTASE / SULFATE REDUCTION
Function / homology
Function and homology information


dissimilatory sulfite reductase (NADH) activity / sulfite reductase activity / sulfite reductase (ferredoxin) activity / sulfur carrier activity / sulfite reductase complex (NADPH) / tRNA wobble position uridine thiolation / sulfate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding ...dissimilatory sulfite reductase (NADH) activity / sulfite reductase activity / sulfite reductase (ferredoxin) activity / sulfur carrier activity / sulfite reductase complex (NADPH) / tRNA wobble position uridine thiolation / sulfate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / cytoplasm
Similarity search - Function
DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Sulphite reductase, dissimilatory-type beta subunit / Alpha-Beta Plaits - #2500 ...DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Sulphite reductase, dissimilatory-type beta subunit / Alpha-Beta Plaits - #2500 / Helix Hairpins - #1420 / Sulphite reductase, dissimilatory-type alpha subunit / Alpha-Beta Plaits - #3340 / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / Helix Hairpins / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / SULFITE ION / SIROHEME / Sulfite reductase beta / Sulfite reductase alpha / Sulfite redcutase subunit gama
Similarity search - Component
Biological speciesdesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHsieh, Y.C. / Liu, M.Y. / Wang, V.C.C. / Chiang, Y.L. / Liu, E.H. / Wu, W.G. / Chan, S.I. / Chen, C.J.
CitationJournal: To be Published
Title: Dissimilatory Sulfite Reductase, Sulfate Reduction
Authors: 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.
History
DepositionSep 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Dec 27, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfite redcutase subunit alpha
B: Sulfite redcutase subunit beta
C: Sulfite redcutase subunit gama
D: Sulfite redcutase subunit alpha
E: Sulfite redcutase subunit beta
F: Sulfite redcutase subunit gama
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,42122
Polymers205,6216
Non-polymers6,80016
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44740 Å2
ΔGint-243 kcal/mol
Surface area59450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.129, 59.977, 133.208
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Sulfite redcutase subunit ... , 3 types, 6 molecules ADBECF

#1: Protein Sulfite redcutase subunit alpha


Mass: 48797.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) desulfovibrio gigas (bacteria) / References: UniProt: E2QR97*PLUS
#2: Protein Sulfite redcutase subunit beta


Mass: 42792.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) desulfovibrio gigas (bacteria) / References: UniProt: E2QR96*PLUS
#3: Protein Sulfite redcutase subunit gama


Mass: 11220.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) desulfovibrio gigas (bacteria) / References: UniProt: E2QR99*PLUS

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Non-polymers , 4 types, 697 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO3
#6: Chemical
ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THREE ENTITIES DO NOT CURRENTLY EXIST. THE AUTHOR WILL BE ...THE SEQUENCE DATABASE REFERENCES FOR THREE ENTITIES DO NOT CURRENTLY EXIST. THE AUTHOR WILL BE SUBMITTED THE SEQUENCE TO THE DATABASE IN THE FUTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONNSRRC BL13B11
SYNCHROTRONSPring-8 BL26B22
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 5, 2009
ADSC QUANTUM 315r2CCDFeb 23, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 112128 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Rsym value: 0.067 / Net I/σ(I): 15.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.25 / % possible all: 83.1

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OR1

3or1


Resolution: 2.05→30 Å
RfactorNum. reflection
Rfree0.219 -
Rwork0.191 -
obs0.191 112112
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14418 0 328 681 15427

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