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- PDB-1ykg: Solution structure of the flavodoxin-like domain from the Escheri... -

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Basic information

Entry
Database: PDB / ID: 1ykg
TitleSolution structure of the flavodoxin-like domain from the Escherichia coli sulfite reductase
ComponentsSulfite reductase [NADPH] flavoprotein alpha-component
KeywordsELECTRON TRANSPORT / flavoprotein
Function / homology
Function and homology information


assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase complex (NADPH) / riboflavin reductase (NADPH) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / L-cysteine biosynthetic process / NADP+ binding / FMN binding / flavin adenine dinucleotide binding ...assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase complex (NADPH) / riboflavin reductase (NADPH) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / L-cysteine biosynthetic process / NADP+ binding / FMN binding / flavin adenine dinucleotide binding / oxidoreductase activity / cytosol
Similarity search - Function
Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Flavodoxin domain / 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. ...Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / Flavodoxin domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Sulfite reductase [NADPH] flavoprotein alpha-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSibille, N. / Blackledge, M. / Brutscher, B. / Coves, J. / Bersch, B.
Citation
Journal: Biochemistry / Year: 2005
Title: Solution Structure of the Sulfite Reductase Flavodoxin-like Domain from Escherichia coli
Authors: Sibille, N. / Blackledge, M. / Brutscher, B. / Coves, J. / Bersch, B.
#1: Journal: Biochemistry / Year: 2002
Title: Reactivity, secondary structure, and molecular topology of the Escherichia coli sulfite reductase flavodoxin-like domain
Authors: Champier, L. / Sibille, N. / Bersch, B. / Brutscher, B. / Blackledge, M. / Coves, J.
#2: Journal: J.BIOMOL.NMR / Year: 2001
Title: 1H, 13C, and 15N assignment of the flavodoxin-like domain of the Escherichia coli sulfite reductase
Authors: Sibille, N. / Coves, J. / Marion, D. / Brutscher, B. / Bersch, B.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3482
Polymers17,8911
Non-polymers4561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 15initial selection based on experimental energy target function
RepresentativeModel #2fewest violations

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Components

#1: Protein Sulfite reductase [NADPH] flavoprotein alpha-component / SIR-FP


Mass: 17891.205 Da / Num. of mol.: 1 / Fragment: SiR-FP18, flavodoxin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cysJ / Plasmid: pet30 / Production host: Escherichia coli (E. coli)
References: UniProt: P38038, assimilatory sulfite reductase (NADPH)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
4113D 15N-separated NOESY
3213D 13C-separated NOESY
7312D NOESY
NMR detailsText: residual dipolar couplings and 3hJNC couplings for the detection of hydrogen-bonds have been measured using 3D-HNCO-type experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM U-15N, U-13C, 80%-2H SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10
21.5mM U-15N, U-13C, SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10
31.5mM U-15N, U-13C, SiR-FP18100mM phosphate buffer pH 7.0, D2O
41.5mM U-15N, SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10
51.5mM U-15N, U-13C, 80%-2H SiR-FP18100mM phosphate buffer pH 7.0, 2mM MgCl2, H2O/D2O 90:10, + 14mg/ml filamentous Pf1 phage
61.5mM U-15N, U-13C, 80%-2H SiR-FP18100mM phosphate buffer pH 7.0, H2O/D2O 90:10, +5% C12E5/hexanol with r=0.96
71.5mM U-15N, SiR-FP18100mM phosphate buffer pH 7.0, D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM phosphate buffer 7ambient 303 K
2100mM phosphate buffer, 2mM MgCl2 7ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.98Accelrys Inc.structure solution
SCULPTOR1Hus, J.C., Blackledge, M.refinement
Felix2000Hare, F.processing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: residues 52-62 and 209-218 are disordered and are not included in the pdb file.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: initial selection based on experimental energy target function
Conformers calculated total number: 15 / Conformers submitted total number: 15

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