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Yorodumi- PDB-1j9g: Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j9g | ||||||
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Title | Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris S64C Mutant, monomer oxidised, at 2.4 Angstrom Resolution | ||||||
Components | Flavodoxin | ||||||
Keywords | ELECTRON TRANSPORT / Alpha-helices / beta-sheet | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Artali, R. / Bombieri, G. / Meneghetti, F. / Gilardi, G. / Sadeghi, S.J. / Cavazzini, D. / Rossi, G.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Comparison of the refined crystal structures of wild-type (1.34 A) flavodoxin from Desulfovibrio vulgaris and the S35C mutant (1.44 A) at 100 K. Authors: Artali, R. / Bombieri, G. / Meneghetti, F. / Gilardi, G. / Sadeghi, S.J. / Cavazzini, D. / Rossi, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j9g.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j9g.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9g ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9g | HTTPS FTP |
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-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: 15694.174 Da / Num. of mol.: 1 / Mutation: S64C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00323 |
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#2: Chemical | ChemComp-FMN / |
#3: 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: 3.11 Å3/Da / Density % sol: 60.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Ammonium Sulphate, Tris HCl Buffer, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 1999 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→28.75 Å / Num. all: 8255 / Num. obs: 8255 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 98.8 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.79 |
Reflection shell | Highest resolution: 2.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→24.35 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1087659.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.13 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→24.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
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Xplor file |
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