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

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Basic information

Entry
Database: PDB / ID: 1ddg
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 / Sulfite reductase [NADPH] flavoprotein alpha-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOL. REPL. / Resolution: 2.01 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 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT
B: SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3265
Polymers84,6592
Non-polymers1,6673
Water9,872548
1
A: SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1152
Polymers42,3291
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2113
Polymers42,3291
Non-polymers8822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.840, 82.540, 105.360
Angle α, β, γ (deg.)79.71, 83.05, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT


Mass: 42329.473 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 3 Å3/Da / Density % sol: 64.79 %
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: BM30A / 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: 2.01→20 Å / Num. all: 76269 / Num. obs: 304582 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 4.5
Reflection
*PLUS
Num. obs: 76269 / Num. measured all: 304582

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Processing

Software
NameClassification
SHELXL-97refinement
REFMACrefinement
ARPmodel building
SHELXmodel building
AMoREphasing
ARP/wARPmodel building
SHELXphasing
RefinementMethod to determine structure: MOL. REPL.
Starting model: SIR60-FL

Resolution: 2.01→10 Å / Num. parameters: 6106 / Num. restraintsaints: 7617 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.289 364 5 %RANDOM
all0.206 6887 --
obs--91 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6612
Refinement stepCycle: LAST / Resolution: 2.01→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6063 0 111 548 6722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.05
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_planar_d0.027
X-RAY DIFFRACTIONs_plane_restr0.02

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