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- PDB-3mm5: Dissimilatory sulfite reductase in complex with the substrate sulfite -

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Basic information

Entry
Database: PDB / ID: 3mm5
TitleDissimilatory sulfite reductase in complex with the substrate sulfite
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
IRON/SULFUR CLUSTER / SULFITE ION / 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: 1.8 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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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
D: Sulfite reductase, dissimilatory-type subunit alpha
E: Sulfite reductase, dissimilatory-type subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,06318
Polymers178,4234
Non-polymers6,64014
Water17,493971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34710 Å2
ΔGint-208 kcal/mol
Surface area50000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 68.900, 145.100
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
12D
22A
13B
23E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVAL6AA1 - 3862 - 387
211SERSERVALVAL6DC1 - 3862 - 387
121SF4SF4SRMSRM4AF - E575 - 580
221SF4SF4SRMSRM4DM - L575 - 580
112LYSLYSTRPTRP6DC387 - 417388 - 418
212LYSLYSTRPTRP6AA387 - 417388 - 418
113GLUGLUTRPTRP6BB4 - 3664 - 366
213GLUGLUTRPTRP6ED4 - 3664 - 366
123SRMSRMSF4SF44BK - J570 - 586
223SRMSRMSF4SF44ER - Q570 - 586

NCS ensembles :
ID
2
1
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, 985 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-SO3 / SULFITE ION


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


Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.23 %
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, 50 mM Na2SO3, 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: X06SA / Wavelength: 0.99989 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.64 % / Rmerge(I) obs: 0.14 / Rsym value: 0.131 / Net I/σ(I): 7.04
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.05 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.54 / Num. unique all: 86856 / Rsym value: 0.583 / % possible all: 94.4

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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: 1.8→15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.248 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18766 8181 5 %RANDOM
Rwork0.15836 ---
all0.15982 155432 --
obs0.15982 155432 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: 11.527 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12462 0 324 971 13757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213242
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.99218082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21451572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83923.875578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.289152230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1771576
X-RAY DIFFRACTIONr_chiral_restr0.1410.21885
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110112
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3045LOOSE POSITIONAL0.315
1A3045LOOSE THERMAL1.5310
2D261LOOSE POSITIONAL0.45
2D261LOOSE THERMAL510
3B2872LOOSE POSITIONAL0.325
3B2872LOOSE THERMAL2.1810
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 579 -
Rwork0.244 10993 -
obs-10993 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.07770.0902-0.021.1571-0.01010.4845-0.02770.06590.0089-0.0960.0249-0.03310.0050.00390.00280.0301-0.0005-0.03260.03390.00390.060246.6313.26661.117
21.2207-0.0086-0.23921.45020.0380.8660.05790.62960.1035-0.8376-0.0553-0.3832-0.02290.1102-0.00250.740.02720.24810.61750.1030.206568.38421.12617.388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 386
2X-RAY DIFFRACTION1B4 - 366
3X-RAY DIFFRACTION1D387 - 417
4X-RAY DIFFRACTION2A387 - 417
5X-RAY DIFFRACTION2D1 - 386
6X-RAY DIFFRACTION2E4 - 366

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