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- PDB-4g39: Mutational analysis of sulfite reductase hemoprotein reveals the ... -

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Basic information

Entry
Database: PDB / ID: 4g39
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 / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 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: 2.4 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)65,4626
Polymers64,0211
Non-polymers1,4415
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.598, 77.045, 86.851
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: 64020.977 Da / Num. of mol.: 1
Fragment: sulfite reductase hemoprotein (unp residues 81-570)
Mutation: R153S
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, 122 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.: 2 / 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.: 117 / 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: 1.8 Å3/Da / Density % sol: 30.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 65 mM KPi/22% PEG8000, 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: Oct 16, 2011
RadiationMonochromator: Sagittally-focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 23255 / % possible obs: 85.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.591.70.352141.3
2.59-2.6920.35161.3
2.69-2.812.30.299176.3
2.81-2.962.90.291192.1
2.96-3.153.40.223197.6
3.15-3.393.80.152198.5
3.39-3.733.90.105198.1
3.73-4.263.90.07198
4.26-5.353.90.055197.3
5.35-203.70.039195.9

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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: 2.4→20 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.59 / σ(F): 0.19 / Phase error: 23.17 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2375 1505 8.6 %
Rwork0.1726 --
obs0.1782 17495 95.56 %
all-15378 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.79 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.4948 Å2-0 Å2-0 Å2
2---5.927 Å2-0 Å2
3----8.5678 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 78 117 3847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013847
X-RAY DIFFRACTIONf_angle_d1.3165236
X-RAY DIFFRACTIONf_dihedral_angle_d15.2851440
X-RAY DIFFRACTIONf_chiral_restr0.078563
X-RAY DIFFRACTIONf_plane_restr0.005681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.29321170.19581239X-RAY DIFFRACTION84
2.4775-2.5660.26871250.19181336X-RAY DIFFRACTION89
2.566-2.66880.31211300.18171376X-RAY DIFFRACTION93
2.6688-2.79020.28571340.18821429X-RAY DIFFRACTION96
2.7902-2.93730.28111390.18091467X-RAY DIFFRACTION97
2.9373-3.12130.25681400.19291487X-RAY DIFFRACTION98
3.1213-3.36220.24891390.17731490X-RAY DIFFRACTION99
3.3622-3.70040.23671410.16591486X-RAY DIFFRACTION98
3.7004-4.23540.19051420.1521517X-RAY DIFFRACTION98
4.2354-5.33470.18571440.14881534X-RAY DIFFRACTION99
5.3347-43.86530.23731540.18581629X-RAY DIFFRACTION99

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