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Yorodumi- PDB-1xyy: Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xyy | ||||||
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Title | Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, homodimer, oxidised state | ||||||
Components | FLAVODOXIN | ||||||
Keywords | ELECTRON TRANSPORT / FLAVODOXIN / S64C MUTANT / DIMER / OXIDIZED FORM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Artali, R. / Marchini, N. / Meneghetti, F. / Cavazzini, D. / Bombieri, G. / Rossi, G.L. / Gilardi, G. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Redox properties and crystal structures of a Desulfovibrio vulgaris flavodoxin mutant in the monomeric and homodimeric forms. Authors: Fantuzzi, A. / Artali, R. / Bombieri, G. / Marchini, N. / 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 | 1xyy.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xyy.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/1xyy ftp://data.pdbj.org/pub/pdb/validation_reports/xy/1xyy | HTTPS FTP |
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-Related structure data
Related structure data | 1wsbC 1wswC 1xyvC 1j9gS 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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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -y, -x, -z+1/2 |
-Components
#1: Protein | Mass: 15825.371 Da / Num. of mol.: 1 / Mutation: S64C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Plasmid: pT7 / Production host: Desulfovibrio vulgaris (bacteria) / References: UniProt: P00323 |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS MAINTAIN THAT RESIDUE 2 IS ALA AND NOT PRO. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Ammonium Sulphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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: CCD / Date: Dec 12, 2003 |
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: 1.66→41.17 Å / Num. all: 21484 / Num. obs: 13063 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 4.1 Å2 / Rsym value: 0.127 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.9 % / Rsym value: 0.241 / % possible all: 99.9 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J9G Resolution: 1.7→19.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1241568.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 20 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 91.9085 Å2 / ksol: 0.504138 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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