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- PDB-3mm7: Dissimilatory sulfite reductase carbon monoxide complex -

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Basic information

Entry
Database: PDB / ID: 3mm7
TitleDissimilatory sulfite reductase carbon monoxide complex
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
CARBON MONOXIDE / 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: 1.9 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.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

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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)184,93117
Polymers178,4234
Non-polymers6,50813
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34970 Å2
ΔGint-208 kcal/mol
Surface area51150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.840, 69.280, 146.330
Angle α, β, γ (deg.)90.00, 107.68, 90.00
Int Tables number4
Space group name H-MP1211

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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, 525 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
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 KCN, 1 bar CO, 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: 1.0001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.164 / Rsym value: 0.133 / Net I/σ(I): 9
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.76 / Num. unique all: 59934 / Rsym value: 0.658 / % possible all: 99.7

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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: 1.9→49.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.015 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26118 7021 5 %RANDOM
Rwork0.21504 ---
all0.21737 133609 --
obs0.21737 133609 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å22.35 Å2
2---2.28 Å20 Å2
3---4.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12462 0 318 512 13292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02213189
X-RAY DIFFRACTIONr_angle_refined_deg2.2531.99118000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41151556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80123.763574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.172152214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0841578
X-RAY DIFFRACTIONr_chiral_restr0.1740.21878
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02110062
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 497 -
Rwork0.373 9898 -
obs-9898 99.71 %
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)
11.23760.115-0.08371.3545-0.01930.475-0.03150.0838-0.0472-0.10870.0314-0.15730.01830.034200.0845-0.0035-0.02080.10460.00180.047446.27211.78460.292
20.7020.1618-0.06161.14890.35931.3378-0.04870.61780.0516-0.75860.0866-0.3849-0.04780.2563-0.03790.7308-0.05160.21570.74620.08180.351468.122.78518.181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 417
2X-RAY DIFFRACTION1B4 - 366
3X-RAY DIFFRACTION2D1 - 417
4X-RAY DIFFRACTION2E4 - 366

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