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Yorodumi- PDB-1j8q: Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j8q | ||||||
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Title | Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris Wild-type at 1.35 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 / AB INITIO PHASING / Resolution: 1.35 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 | 1j8q.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j8q.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1j8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j8q_validation.pdf.gz | 759.9 KB | Display | wwPDB validaton report |
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Full document | 1j8q_full_validation.pdf.gz | 762.6 KB | Display | |
Data in XML | 1j8q_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1j8q_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/1j8q ftp://data.pdbj.org/pub/pdb/validation_reports/j8/1j8q | HTTPS FTP |
-Related structure data
Related structure data | 1j9eC 1j9gC 3fx2S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 15678.109 Da / Num. of mol.: 1 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: 56.38 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium Sulphate, Tris HCl Buffer, pH 7.0, 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: 1.35→28.51 Å / Num. all: 40361 / Num. obs: 38342 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 24.697 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.61 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.256 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: PDB ENTRY 3FX2 Resolution: 1.35→28.513 Å / Num. parameters: 1185 / Num. restraintsaints: 1412 / 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: 1028 / Occupancy sum non hydrogen: 1317 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→28.513 Å
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Refine LS restraints |
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