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Yorodumi- PDB-3vya: W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vya | ||||||
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Title | W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) | ||||||
Components | FMN-binding protein | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Takagi, R. / Nakanishi, T. / Kitamura, M. | ||||||
Citation | Journal: To be Published Title: Crystal structure of W32Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) Authors: Takagi, R. / Nakanishi, T. / Kitamura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vya.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vya.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vya_validation.pdf.gz | 749.7 KB | Display | wwPDB validaton report |
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Full document | 3vya_full_validation.pdf.gz | 750.3 KB | Display | |
Data in XML | 3vya_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 3vya_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vya ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vya | HTTPS FTP |
-Related structure data
Related structure data | 1flmS 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: 13130.030 Da / Num. of mol.: 1 / Mutation: W32Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / Gene: DvMF_2023 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46604 |
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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: 1.91 Å3/Da / Density % sol: 35.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.05 Details: 100mM HEPES, 85%(v/v) 2-Methyl-2,4-pentanediol, 50%(w/v) polyethylene glycol 400, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 4587 / % possible obs: 99.8 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.128 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 15 % / Rmerge(I) obs: 0.258 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLM Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.874 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.747 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.796 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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