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- PDB-1ddi: CRYSTAL STRUCTURE OF SIR-FP60 -

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Basic information

Entry
Database: PDB / ID: 1ddi
TitleCRYSTAL STRUCTURE OF SIR-FP60
ComponentsSULFITE REDUCTASE [NADPH] FLAVOPROTEIN ALPHA-COMPONENT
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 REDUCTASE / FNR / FLAVOPROTEIN / MODULAR PROTEIN
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 / 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 / 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 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like ...Sulphite reductase [NADPH] flavoprotein, alpha chain / Sulphite reductase [NADPH] flavoprotein, alpha chain, Proteobacteria / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Sulfite reductase [NADPH] flavoprotein alpha-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.51 Å
AuthorsGruez, A. / Pignol, D. / Zeghouf, M. / Coves, J. / Fontecave, M. / Ferrer, J.L. / Fontecilla-Camps, J.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Four crystal structures of the 60 kDa flavoprotein monomer of the sulfite reductase indicate a disordered flavodoxin-like module.
Authors: Gruez, A. / Pignol, D. / Zeghouf, M. / Coves, J. / Fontecave, M. / Ferrer, J.L. / Fontecilla-Camps, J.C.
History
DepositionNov 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 7, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / reflns ...refine / reflns / struct_sheet / struct_site
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs ..._refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct / _reflns.number_all / _reflns.number_obs / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,8583
Polymers42,3291
Non-polymers1,5292
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.610, 98.610, 123.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SULFITE REDUCTASE [NADPH] FLAVOPROTEIN ALPHA-COMPONENT


Mass: 42329.473 Da / Num. of mol.: 1 / Fragment: SIR-FP60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P38038, assimilatory sulfite reductase (NADPH)
#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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
22.5 mMNADP+1drop
350 mMTris-HCl1reservoirpH7.0
42 Mammonium sulfate1reservoir
510 %(w/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→20 Å / Num. obs: 23679 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.2
Reflection
*PLUS
Num. obs: 23679 / Num. measured all: 212439

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.51→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.245 1150 5 %
Rwork0.185 --
all-23679 -
obs-23679 98.4 %
Refinement stepCycle: LAST / Resolution: 2.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 79 271 3246
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor all: 0.1852
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d0.036

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