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- PDB-3mmb: Dissimilatory sulfite reductase in complex with the endproduct sulfide -

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Basic information

Entry
Database: PDB / ID: 3mmb
TitleDissimilatory sulfite reductase in complex with the endproduct sulfide
Components(Sulfite reductase, dissimilatory-type subunit ...) x 2
KeywordsOXIDOREDUCTASE / alpha-beta-protein
Function / homology
Function and homology information


dissimilatory sulfite reductase system / dissimilatory sulfite reductase activity / sulfur compound metabolic process / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / membrane / metal ion binding
Similarity search - Function
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 ...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 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROSULFURIC ACID / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase, dissimilatory-type subunit alpha / Sulfite reductase, dissimilatory-type subunit beta
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsParey, K. / Warkentin, E. / Kroneck, P.M.H. / Ermler, U.
CitationJournal: Biochemistry / Year: 2010
Title: Reaction cycle of the dissimilatory sulfite reductase from Archaeoglobus fulgidus.
Authors: Parey, K. / Warkentin, E. / Kroneck, P.M. / Ermler, U.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfite reductase, dissimilatory-type subunit alpha
B: Sulfite reductase, dissimilatory-type subunit beta
D: Sulfite reductase, dissimilatory-type subunit alpha
E: Sulfite reductase, dissimilatory-type subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,93717
Polymers178,4234
Non-polymers6,51413
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35290 Å2
ΔGint-208 kcal/mol
Surface area50550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.800, 68.500, 146.500
Angle α, β, γ (deg.)90.00, 107.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13D
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 174
2112D1 - 174
1212A176
2212D176
1312A185 - 218
2312D185 - 218
1412A220 - 222
2412D220 - 222
1512A224 - 386
2512D224 - 386
1614A2570 - 2576
2614D2570 - 2576
1122B4 - 180
2122E4 - 180
1222B366 - 1184
2222E366 - 1184
1324B2580 - 2586
2324E2580 - 2586
1132D387 - 417
2132A387 - 417

NCS ensembles :
ID
1
2
3

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Components

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Sulfite reductase, dissimilatory-type subunit ... , 2 types, 4 molecules ADBE

#1: Protein Sulfite reductase, dissimilatory-type subunit alpha / Hydrogensulfite reductase subunit alpha


Mass: 47589.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: Q59109, EC: 1.8.99.3
#2: Protein Sulfite reductase, dissimilatory-type subunit beta / Hydrogensulfite reductase subunit beta


Mass: 41621.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: Q59110, EC: 1.8.99.3

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Non-polymers , 4 types, 127 molecules

#3: Chemical
ChemComp-SRM / SIROHEME


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


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 100 mM Na-citrate, 0.2 M NaCl, 5% (v/v) 2-propanol, 10 mM Na2S, 10 mM Cr(II) EDTA , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 3, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rmerge(I) obs: 0.126 / Rsym value: 0.106 / Net I/σ(I): 8.55
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.2 / Num. unique all: 7231 / Rsym value: 0.268 / % possible all: 91.4

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Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.6.0046refinement
XDSdata reduction
XDSdata scaling
REFMAC5.6.0046phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C7B

3c7b
PDB Unreleased entry


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.812 / SU B: 23.88 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30187 3960 5 %RANDOM
Rwork0.25483 ---
all0.25717 75242 --
obs0.25717 75242 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.29 Å2
2---0.47 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12462 0 317 114 12893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.99118000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94751556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64123.763574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.634152214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7691578
X-RAY DIFFRACTIONr_chiral_restr0.1130.21878
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110062
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1500TIGHT POSITIONAL0.20.05
1A1569MEDIUM POSITIONAL0.430.5
1A1500TIGHT THERMAL1.430.5
1A1569MEDIUM THERMAL1.622
2B712TIGHT POSITIONAL0.250.05
2B797MEDIUM POSITIONAL0.490.5
2B712TIGHT THERMAL1.880.5
2B797MEDIUM THERMAL2.562
3D124TIGHT POSITIONAL0.330.05
3D143MEDIUM POSITIONAL0.550.5
3D124TIGHT THERMAL4.730.5
3D143MEDIUM THERMAL4.612
1A1500TIGHT POSITIONAL0.20.05
1A712TIGHT POSITIONAL0.250.05
1A124TIGHT POSITIONAL0.330.05
1A1569MEDIUM POSITIONAL0.430.5
1A797MEDIUM POSITIONAL0.490.5
1A143MEDIUM POSITIONAL0.550.5
1A1500TIGHT THERMAL1.430.5
1A712TIGHT THERMAL1.880.5
1A124TIGHT THERMAL4.730.5
1A1569MEDIUM THERMAL1.622
1A797MEDIUM THERMAL2.562
1A143MEDIUM THERMAL4.612
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 275 -
Rwork0.287 5241 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 57.349 Å / Origin y: 17.024 Å / Origin z: 39.402 Å
111213212223313233
T0.2531 Å2-0.01 Å20.0299 Å2-0.2618 Å2-0.0002 Å2--0.0968 Å2
L0.8854 °20.1526 °2-0.1551 °2-0.8862 °2-0.0876 °2--0.5362 °2
S-0.0384 Å °0.3894 Å °0.0055 Å °-0.4102 Å °0.0517 Å °-0.1852 Å °0.0229 Å °0.096 Å °-0.0133 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 417
2X-RAY DIFFRACTION1B4 - 366
3X-RAY DIFFRACTION1D1 - 417
4X-RAY DIFFRACTION1E4 - 366

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