+Open data
-Basic information
Entry | Database: PDB / ID: 1ddi | ||||||
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Title | CRYSTAL STRUCTURE OF SIR-FP60 | ||||||
Components | SULFITE REDUCTASE [NADPH] FLAVOPROTEIN ALPHA-COMPONENT | ||||||
Keywords | OXIDOREDUCTASE / 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.51 Å | ||||||
Authors | Gruez, A. / Pignol, D. / Zeghouf, M. / Coves, J. / Fontecave, M. / Ferrer, J.L. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddi.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddi.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ddi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ddi_validation.pdf.gz | 536 KB | Display | wwPDB validaton report |
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Full document | 1ddi_full_validation.pdf.gz | 569.3 KB | Display | |
Data in XML | 1ddi_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1ddi_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddi ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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) |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.06 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.51→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.51→20 Å
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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
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