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Yorodumi- PDB-1wli: L122Y mutant of FMN-binding protein from Desulfovibrio vulgaris (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wli | ||||||
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Title | L122Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) | ||||||
Components | FMN-binding protein | ||||||
Keywords | ELECTRON TRANSPORT / Flavoprotein / FMN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.6 Å | ||||||
Authors | Shibata, N. / Higuchi, Y. | ||||||
Citation | Journal: J.Biochem. / Year: 2007 Title: Determination of the role of the Carboxyl-terminal leucine-122 in FMN-binding protein by mutational and structural analysis. Authors: Kitamura, M. / Terakawa, K. / Inoue, H. / Hayashida, T. / Suto, K. / Morimoto, Y. / Yasuoka, N. / Shibata, N. / Higuchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wli.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wli.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/1wli ftp://data.pdbj.org/pub/pdb/validation_reports/wl/1wli | HTTPS FTP |
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-Related structure data
Related structure data | 1wlkC 3a20C 1flmS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 13203.083 Da / Num. of mol.: 2 / Mutation: L122Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: Miyazaki F / Production host: Escherichia coli (E. coli) / References: UniProt: Q46604 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU |
Detector | Type: OXFORD / Detector: CCD / Date: Dec 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.6 Å / Num. all: 29692 / Num. obs: 29692 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: 1FLM Resolution: 1.6→8 Å / Num. parameters: 8895 / Num. restraintsaints: 8133 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2177 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rwork: 0.157 |