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- PDB-3or1: Crystal structure of dissimilatory sulfite reductase I (DsrI) -

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Basic information

Entry
Database: PDB / ID: 3or1
TitleCrystal structure of dissimilatory sulfite reductase I (DsrI)
Components(Sulfite reductase ...) x 3
KeywordsOXIDOREDUCTASE / Dissimilatory sulfite reductase / sulfate reduction / sulfite reduction
Function / homology
Function and homology information


dissimilatory sulfite reductase activity / sulfur compound metabolic process / 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 / Alpha-Beta Plaits - #3340 / Helix Hairpins - #1420 / Sulphite reductase, dissimilatory-type alpha subunit / 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 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / Helix Hairpins / 4Fe-4S dicluster domain / 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 reductase gama
Similarity search - Component
Biological speciesdesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 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: Structure insights into the enzyme catalysis from comparison of three forms of dissimilatory sulfite reductase from Desulfovibrio gigas
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 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)213,10620
Polymers206,4666
Non-polymers6,64014
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44730 Å2
ΔGint-240 kcal/mol
Surface area58920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.721, 60.478, 132.915
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Sulfite reductase ... , 3 types, 6 molecules ADBECF

#1: Protein Sulfite reductase alpha


Mass: 48999.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) desulfovibrio gigas (bacteria) / References: UniProt: E2QR97*PLUS
#2: Protein Sulfite reductase beta


Mass: 42923.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) desulfovibrio gigas (bacteria) / References: UniProt: E2QR96*PLUS
#3: Protein Sulfite reductase gama


Mass: 11309.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) desulfovibrio gigas (bacteria) / References: UniProt: E2QR98*PLUS

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Non-polymers , 4 types, 743 molecules

#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#5: Chemical
ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 44.77 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 23%(W/V) PEG6000, 200MM SODIUM CHLORIDE, 100MM MES BUFFER, pH 5.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONSPring-8 BL26B221.73772, 1.74137, 1.69379, 1.760
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 10, 2008
RIGAKU JUPITER 2102CCDJan 27, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.737721
31.741371
41.693791
51.761
ReflectionResolution: 1.76→30 Å / Num. obs: 179998 / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Rsym value: 0.061 / Net I/σ(I): 18.7
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.359 / % possible all: 99.3

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.76→30 Å
RfactorNum. reflection
Rfree0.212 -
Rwork0.193 -
obs0.193 179998
Refinement stepCycle: LAST / Resolution: 1.76→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14416 0 322 729 15467

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