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- PDB-4g38: Mutational analysis of sulfite reductase hemoprotein reveals the ... -

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Basic information

Entry
Database: PDB / ID: 4g38
TitleMutational analysis of sulfite reductase hemoprotein reveals the mechanism for coordinated electron and proton transfer
ComponentsSulfite reductase [NADPH] hemoprotein beta-component
KeywordsOXIDOREDUCTASE / SNiRR / sulfite reductase flavoprotein
Function / homology
Function and homology information


assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding ...assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding
Similarity search - Function
Sulphite reductase (NADPH) hemoprotein, beta subunit / Sulfite Reductase Hemoprotein;Domain 2 / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Sulfite Reductase Hemoprotein; domain 2 / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / 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 (NADPH) hemoprotein, beta subunit / Sulfite Reductase Hemoprotein;Domain 2 / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Sulfite Reductase Hemoprotein; domain 2 / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase [NADPH] hemoprotein beta-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 Å
AuthorsSmith, K.W. / Stroupe, M.E.
CitationJournal: Biochemistry / Year: 2012
Title: Mutational analysis of sulfite reductase hemoprotein reveals the mechanism for coordinated electron and proton transfer.
Authors: Smith, K.W. / Stroupe, M.E.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Feb 28, 2024Group: 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 / entity / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / 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_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _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 [NADPH] hemoprotein beta-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5665
Polymers64,1631
Non-polymers1,4024
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.327, 76.171, 81.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfite reductase [NADPH] hemoprotein beta-component / SiR-HP / SiRHP


Mass: 64163.203 Da / Num. of mol.: 1
Fragment: sulfite reductase hemoprotein (unp residues 74-570)
Mutation: N149W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2763, cysI, JW2733 / Plasmid: pBAD/myc-hisA / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
References: UniProt: P17846, assimilatory sulfite reductase (NADPH)

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Non-polymers , 5 types, 568 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 1.6 Å3/Da / Density % sol: 24.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 65 mM KPi/22% PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: Sagitally Focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 57746 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.56-1.663.20.214191.8
2.14-2.183.60.243183.1
2.18-2.223.70.24188
2.22-2.263.90.262192.4
2.26-2.3140.25193.8
2.31-2.374.10.251196.6
2.37-2.424.30.255198.3
2.42-2.494.50.256198.9
2.49-2.564.70.236199.5
2.56-2.6550.23199.2
2.65-2.745.30.223199.4
2.74-2.855.60.218199.8
2.85-2.985.80.1871100
2.98-3.1460.1521100
3.14-3.3360.1181100
3.33-3.596.10.1041100
3.59-3.9560.0941100
3.95-4.5260.082199.6
4.52-5.760.077198
5.7-505.80.091194.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.11data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→22.767 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.37 / σ(F): 0.1 / Phase error: 15.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1775 1993 3.45 %
Rwork0.1402 --
obs0.1414 57746 97.15 %
all-25272 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.048 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9417 Å2-0 Å2-0 Å2
2---2.9755 Å2-0 Å2
3----1.9662 Å2
Refinement stepCycle: LAST / Resolution: 1.56→22.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 77 564 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083726
X-RAY DIFFRACTIONf_angle_d1.6565071
X-RAY DIFFRACTIONf_dihedral_angle_d14.5291380
X-RAY DIFFRACTIONf_chiral_restr0.083546
X-RAY DIFFRACTIONf_plane_restr0.006658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5596-1.59860.20611290.1523720X-RAY DIFFRACTION92
1.5986-1.64180.19161390.13913831X-RAY DIFFRACTION95
1.6418-1.69010.19271340.12293836X-RAY DIFFRACTION95
1.6901-1.74460.16931410.11823889X-RAY DIFFRACTION96
1.7446-1.8070.17351350.1163894X-RAY DIFFRACTION96
1.807-1.87930.17611420.11913921X-RAY DIFFRACTION97
1.8793-1.96480.16711410.12293956X-RAY DIFFRACTION97
1.9648-2.06830.16721430.13114003X-RAY DIFFRACTION98
2.0683-2.19780.16961320.13524047X-RAY DIFFRACTION99
2.1978-2.36730.16731540.13594035X-RAY DIFFRACTION99
2.3673-2.60520.19191480.14434051X-RAY DIFFRACTION99
2.6052-2.98150.17531500.15714094X-RAY DIFFRACTION99
2.9815-3.75360.16391500.14744162X-RAY DIFFRACTION100
3.7536-22.76980.19311550.15124314X-RAY DIFFRACTION99

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