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Yorodumi- PDB-3vy2: N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vy2 | ||||||
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Title | N33D 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: 1.6 Å | ||||||
Authors | Takagi, R. / Nakanishi, T. / Kitamura, M. | ||||||
Citation | Journal: To be Published Title: Crystal structure of N33D 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 | 3vy2.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vy2.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 3vy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vy2_validation.pdf.gz | 1019.2 KB | Display | wwPDB validaton report |
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Full document | 3vy2_full_validation.pdf.gz | 1020.9 KB | Display | |
Data in XML | 3vy2_validation.xml.gz | 14 KB | Display | |
Data in CIF | 3vy2_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vy2 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vy2 | 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: 13154.052 Da / Num. of mol.: 2 / Mutation: N33D 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 #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: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 23% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19.8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2010 |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 31712 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.196 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLM Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.285 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.084 / 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: 18.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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