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Yorodumi- PDB-1j9e: Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j9e | ||||||
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Title | Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris S35C Mutant at 1.44 Angstrom Resolution | ||||||
Components | FLAVODOXIN | ||||||
Keywords | ELECTRON TRANSPORT / alpha-helices / beta-sheets | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.44 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 | 1j9e.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j9e.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j9e_validation.pdf.gz | 732.2 KB | Display | wwPDB validaton report |
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Full document | 1j9e_full_validation.pdf.gz | 734.3 KB | Display | |
Data in XML | 1j9e_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1j9e_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9e ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9e | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15694.174 Da / Num. of mol.: 1 / Mutation: S35C 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: 2 Å3/Da / Density % sol: 56.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium sulphate, tris-HCl buffer, pH 7.00, VAPOR DIFFUSION, HANGING 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: 1.44→16.37 Å / Num. all: 3232 / Num. obs: 3099 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 13.027 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.44→16.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.046 / % possible all: 95.3 |
Reflection | *PLUS % possible obs: 96 % / Num. measured all: 29127 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.44→16.37 Å / Num. parameters: 1175 / Num. restraintsaints: 2033 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 1030 / Occupancy sum non hydrogen: 1305 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→16.37 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 11 % / Rfactor obs: 0.136 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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