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- PDB-2v4j: THE CRYSTAL STRUCTURE OF Desulfovibrio vulgaris DISSIMILATORY SUL... -

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Entry
Database: PDB / ID: 2v4j
TitleTHE CRYSTAL STRUCTURE OF Desulfovibrio vulgaris DISSIMILATORY SULFITE REDUCTASE BOUND TO DsrC PROVIDES NOVEL INSIGHTS INTO THE MECHANISM OF SULFATE RESPIRATION
Components(SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ...) x 3
KeywordsOXIDOREDUCTASE / DISSIMILATORY SULFITE REDUCTASE / SIROHEME / SIROHYDROCHLORIN
Function / homology
Function and homology information


dissimilatory sulfite reductase system / dissimilatory sulfite reductase activity / sulfur carrier activity / tRNA wobble position uridine thiolation / 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 / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 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 / Chem-SH0 / SULFITE ION / SIROHEME / Sulfite reductase, dissimilatory-type subunit gamma / Sulfite reductase, dissimilatory-type subunit alpha / Sulfite reductase, dissimilatory-type subunit beta
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsOliveira, T.F. / Vonrhein, C. / Matias, P.M. / Venceslau, S.S. / Pereira, I.A.C. / Archer, M.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: The Crystal Structure of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound to Dsrc Provides Novel Insights Into the Mechanism of Sulfate Respiration.
Authors: Oliveira, T.F. / Vonrhein, C. / Matias, P.M. / Venceslau, S.S. / Pereira, I.A.C. / Archer, M.
#1: Journal: J.Struct.Biol. / Year: 2008
Title: Purification, Crystallization and Preliminary Crystallographic Analysis of a Dissimilatory Dsrab Sulfite Reductase in Complex with Dsrc.
Authors: Oliveira, T.F. / Vonrhein, C. / Matias, P.M. / Venceslau, S.S. / Pereira, I.A. / Archer, M.
History
DepositionSep 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Version format compliance
Revision 2.0Dec 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / entity / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / 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_database_status.status_code_sf / _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_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_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ALPHA
B: SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT BETA
C: SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT GAMMA
D: SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ALPHA
E: SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT BETA
F: SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,77720
Polymers207,2326
Non-polymers6,54414
Water18,3031016
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55340 Å2
ΔGint-494.3 kcal/mol
Surface area55140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.410, 118.900, 132.240
Angle α, β, γ (deg.)90.00, 104.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.74146, 0.42737, -0.51729), (0.42442, -0.29841, -0.85488), (-0.51972, -0.85341, 0.03987)29.89904, 51.59716, 57.15992
2given(-0.74232, 0.4279, -0.51562), (0.42428, -0.29542, -0.85599), (-0.5186, -0.85418, 0.03775)29.77774, 51.46428, 57.38292
3given(-0.73239, 0.44772, -0.51298), (0.42937, -0.28102, -0.85829), (-0.52843, -0.84887, 0.01358)28.39294, 50.88845, 57.95444

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Components

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SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ... , 3 types, 6 molecules ADBECF

#1: Protein SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT ALPHA / DISSIMILATORY SULFITE REDUCTASE / DESULFOVIRIDIN SUBUNIT ALPHA / HYDROGENSULFITE REDUCTASE ALPHA SUBUNIT


Mass: 49154.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P45574, EC: 1.8.99.3
#2: Protein SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT BETA / DISSIMILATORY SULFITE REDUCTASE / DESULFOVIRIDIN SUBUNIT BETA / HYDROGENSULFITE REDUCTASE SUBUNIT BETA


Mass: 42574.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P45575, EC: 1.8.99.3
#3: Protein SULFITE REDUCTASE, DISSIMILATORY-TYPE SUBUNIT GAMMA / DISSIMILATORY SULFITE REDUCTASE / DESULFOVIRIDIN SUBUNIT GAMMA / HYDROGENSULFITE REDUCTASE GAMMA SUBUNIT


Mass: 11887.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P45573, EC: 1.8.99.3

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Non-polymers , 5 types, 1030 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-SH0 / 3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,11S,12S,13S,16S,19S)-3,8,13,17-tetrakis(carboxylatomethyl)-8,13-dimethyl-1,2,3,4,7,8,11,12,13,16,19,20,22,24-tetradecahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoate / Sirohydrochlorin


Mass: 868.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H52N4O16
#6: Chemical ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#7: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 12.5% PEG 4000, 0.1M TRIS-HCL PH 8.5, 0.2M MGCL2

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.033, 1.742
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.7421
ReflectionResolution: 2.1→40.29 Å / Num. obs: 112244 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 36.887 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 88.7

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Processing

Software
NameClassification
BUSTER-TNTrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.1→128.04 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 5616 5.01 %RANDOM
Rwork0.1901 ---
obs0.1916 112195 97.89 %-
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.66209431 Å20 Å2-6.25363262 Å2
2--6.27152084 Å20 Å2
3---1.39057347 Å2
Refinement stepCycle: LAST / Resolution: 2.1→128.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14478 0 322 1016 15816
LS refinement shellResolution: 2.1→2.23 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2656 800 4.89 %
Rwork0.2334 15558 -
all0.235 16358 -
obs--97.89 %

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