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Yorodumi- PDB-3a20: L122K mutant of FMN-binding protein from Desulfovibrio vulgaris (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a20 | |||||||||
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Title | L122K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) | |||||||||
Components | FMN-binding protein | |||||||||
Keywords | ELECTRON TRANSPORT / BETA SHEET / Cytoplasm / Flavoprotein / FMN / Transport | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 | 3a20.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a20.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 3a20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a20_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3a20_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3a20_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3a20_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/3a20 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/3a20 | HTTPS FTP |
-Related structure data
Related structure data | 1wliC 1wlkC 1flmS 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
#1: Protein | Mass: 13169.089 Da / Num. of mol.: 2 / Mutation: L122K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) 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: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 6000, 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: 1.6→30 Å / Num. all: 30132 / Num. obs: 30132 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 16.7 / Num. unique all: 2097 / % possible all: 66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLM Resolution: 1.6→25.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 339289.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.1896 Å2 / ksol: 0.381936 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→25.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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