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- PDB-6efv: The NADPH-dependent sulfite reductase flavoprotein adopts an exte... -

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Basic information

Entry
Database: PDB / ID: 6efv
TitleThe NADPH-dependent sulfite reductase flavoprotein adopts an extended conformation that is unique to this diflavin reductase
ComponentsSulfite reductase [NADPH] flavoprotein alpha-component
KeywordsFLAVOPROTEIN / sulfite reductase / sulfite reductase flavoprotein / cytochrome p450 reductase / FAD / FMN / electron transfer
Function / homology
Function and homology information


assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / FMN binding / flavin adenine dinucleotide binding
Similarity search - Function
Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase ...Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Sulfite reductase [NADPH] flavoprotein alpha-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.341 Å
AuthorsTavolieri, A.M. / Askenasy, I. / Murray, D.T. / Pennington, J.M. / Stroupe, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1149763 United States
CitationJournal: J. Struct. Biol. / Year: 2019
Title: NADPH-dependent sulfite reductase flavoprotein adopts an extended conformation unique to this diflavin reductase.
Authors: Tavolieri, A.M. / Murray, D.T. / Askenasy, I. / Pennington, J.M. / McGarry, L. / Stanley, C.B. / Stroupe, M.E.
History
DepositionAug 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfite reductase [NADPH] flavoprotein alpha-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,86811
Polymers63,6071
Non-polymers2,26110
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.483, 99.739, 103.533
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] flavoprotein alpha-component / SiR-FP


Mass: 63607.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: cysJ, A9R57_07045, ACU57_24495, AM266_23140, BHS87_15655, BJJ90_05345, BMT91_11185, BW690_05055, BZL31_00740, C9E25_03405, EL75_0932, EL79_0933, EL80_0936, ERS085365_04603, ERS085416_04655, ...Gene: cysJ, A9R57_07045, ACU57_24495, AM266_23140, BHS87_15655, BJJ90_05345, BMT91_11185, BW690_05055, BZL31_00740, C9E25_03405, EL75_0932, EL79_0933, EL80_0936, ERS085365_04603, ERS085416_04655, ERS139211_04386, ERS150873_02094, GJ11_17940, PGD_04345, RK56_023080
Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
References: UniProt: W8SX42, assimilatory sulfite reductase (NADPH)

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.64 Å3/Da / Density % sol: 53.33 % / Description: Bright yellow octahedron crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 1.8 M Ammonium Sulfate, 100 mM Lithium Sulfate, 100 mM CAPS pH 10.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.341→45.947 Å / Num. obs: 27036 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 24.49 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Χ2: 1.672 / Net I/σ(I): 10.2
Reflection shellResolution: 2.341→2.38 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 8.2 / Num. unique obs: 1320 / CC1/2: 0.969 / Rpim(I) all: 0.102 / Rrim(I) all: 0.259 / Χ2: 0.858 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDG

1ddg


Resolution: 2.341→45.947 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.33
RfactorNum. reflection% reflection
Rfree0.234 1992 7.38 %
Rwork0.1668 --
obs0.1717 26980 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.341→45.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 58 347 4668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074486
X-RAY DIFFRACTIONf_angle_d0.8676121
X-RAY DIFFRACTIONf_dihedral_angle_d14.11661
X-RAY DIFFRACTIONf_chiral_restr0.052665
X-RAY DIFFRACTIONf_plane_restr0.005787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3409-2.39940.2721340.17271693X-RAY DIFFRACTION96
2.3994-2.46430.24941400.16641731X-RAY DIFFRACTION100
2.4643-2.53680.26091490.17251771X-RAY DIFFRACTION100
2.5368-2.61860.24241290.1731786X-RAY DIFFRACTION100
2.6186-2.71220.29371440.17241756X-RAY DIFFRACTION100
2.7122-2.82080.23921390.17211748X-RAY DIFFRACTION100
2.8208-2.94920.22611430.18111791X-RAY DIFFRACTION100
2.9492-3.10460.26381350.1781771X-RAY DIFFRACTION100
3.1046-3.29910.21641440.17461786X-RAY DIFFRACTION100
3.2991-3.55370.24361470.16221808X-RAY DIFFRACTION100
3.5537-3.91120.2191420.15541770X-RAY DIFFRACTION99
3.9112-4.47670.20111470.14021817X-RAY DIFFRACTION100
4.4767-5.63860.21761460.14911828X-RAY DIFFRACTION100
5.6386-45.95540.23641530.19521932X-RAY DIFFRACTION100

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