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- PDB-3mmc: Structure of the dissimilatory sulfite reductase from Archaeoglob... -

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Basic information

Entry
Database: PDB / ID: 3mmc
TitleStructure of the dissimilatory sulfite reductase from Archaeoglobus fulgidus
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 / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / 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 / 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 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 / SIROHEME / Sulfite reductase, dissimilatory-type subunit alpha / Sulfite reductase, dissimilatory-type subunit beta
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.04 Å
AuthorsSchiffer, A. / Parey, K. / Warkentin, E. / Diederichs, K. / Huber, H. / Stetter, K.O. / Kroneck, P.M.H. / Ermler, U.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the dissimilatory sulfite reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus.
Authors: Schiffer, A. / Parey, K. / Warkentin, E. / Diederichs, K. / Huber, H. / Stetter, K.O. / Kroneck, P.M. / Ermler, U.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionMay 12, 2010ID: 3C7B
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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, 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)184,99517
Polymers178,4234
Non-polymers6,57213
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35020 Å2
ΔGint-207 kcal/mol
Surface area50500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.910, 69.260, 147.210
Angle α, β, γ (deg.)90.00, 107.00, 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
1113A1 - 174
2113D1 - 174
1214A2570 - 2576
2214D2570 - 2576
1313A176
2313D176
1413A185 - 218
2413D185 - 218
1513A220 - 222
2513D220 - 222
1613A224 - 386
2613D224 - 386
1123B4 - 180
2123E4 - 180
1223B184 - 366
2223E184 - 366
1324B2585 - 2586
2324E2585 - 2586
1133D387 - 417
2133A387 - 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, 555 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.59 Å3/Da / Density % sol: 52.54 %
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, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9393
SYNCHROTRONEMBL/DESY, HAMBURG BW7A21.733
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 2, 2002
RadiationMonochromator: Diamond (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
21.7331
ReflectionResolution: 2→30 Å / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.087 / Net I/σ(I): 0.074
Reflection shellResolution: 2→2.16 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.391 / % possible all: 79.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.6.0046refinement
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.04→20.11 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.263 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22283 5740 5 %RANDOM
Rwork0.18631 ---
all0.18815 108315 --
obs0.18815 108315 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.29 Å2
2---0.02 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.04→20.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12460 0 322 542 13324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213189
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.99117997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84751556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41523.763574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.865152214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1191578
X-RAY DIFFRACTIONr_chiral_restr0.1370.21878
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110046
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1500TIGHT POSITIONAL0.150.05
1A79MEDIUM POSITIONAL0.710.5
1A1490LOOSE POSITIONAL0.285
1A1500TIGHT THERMAL2.260.5
1A79MEDIUM THERMAL3.082
1A1490LOOSE THERMAL2.910
2B1440TIGHT POSITIONAL0.190.05
2B16MEDIUM POSITIONAL0.120.5
2B1446LOOSE POSITIONAL0.345
2B1440TIGHT THERMAL4.610.5
2B16MEDIUM THERMAL5.152
2B1446LOOSE THERMAL4.7310
3D124TIGHT POSITIONAL0.030.05
3D142LOOSE POSITIONAL0.045
3D124TIGHT THERMAL7.960.5
3D142LOOSE THERMAL6.5410
LS refinement shellResolution: 2.04→2.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 342 -
Rwork0.305 6616 -
obs-6616 82.06 %
Refinement TLS params.Method: refined / Origin x: 57.535 Å / Origin y: 17.097 Å / Origin z: 40.488 Å
111213212223313233
T0.3635 Å2-0.0064 Å20.1101 Å2-0.3282 Å20.0318 Å2--0.1463 Å2
L1.18 °20.0033 °2-0.0035 °2-1.3971 °2-0.0257 °2--0.4168 °2
S-0.0116 Å °0.5714 Å °0.0719 Å °-0.6732 Å °0.0001 Å °-0.3317 Å °-0.0087 Å °0.1075 Å °0.0116 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 417
2X-RAY DIFFRACTION1D1 - 417
3X-RAY DIFFRACTION1B4 - 366
4X-RAY DIFFRACTION1E4 - 366

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