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Yorodumi- PDB-1wlk: L122E mutant of FMN-binding protein from Desulfovibrio vulgaris (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wlk | ||||||
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Title | L122E 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 1wlk.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wlk.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wlk_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1wlk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1wlk_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 1wlk_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/1wlk ftp://data.pdbj.org/pub/pdb/validation_reports/wl/1wlk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13169.022 Da / Num. of mol.: 4 / Mutation: L122E 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 | ChemComp-FMN / #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: 2.05 Å3/Da / Density % sol: 40.03 % |
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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: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→500 Å / Num. all: 33783 / Num. obs: 33783 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 7.3 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 102083.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4564 Å2 / ksol: 0.342761 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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