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Yorodumi- PDB-2e83: T31V mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2.0E+83 | ||||||
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Title | T31V mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) | ||||||
Components | FMN-binding protein | ||||||
Keywords | ELECTRON TRANSPORT / BETA SHEET | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Shibata, N. / Higuchi, Y. | ||||||
Citation | Journal: To be Published Title: Structure of T31V mutant of FMN-binding protein from Desulfovibrio vulgaris Miyazaki F Authors: Shibata, N. / Kitamura, M. / Higuchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e83.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e83.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e83_validation.pdf.gz | 1007.5 KB | Display | wwPDB validaton report |
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Full document | 2e83_full_validation.pdf.gz | 1008.3 KB | Display | |
Data in XML | 2e83_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2e83_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e83 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e83 | 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: 13151.094 Da / Num. of mol.: 2 / Mutation: T31V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: Miyazaki F / Plasmid: pMKBT-100 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / 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: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG 6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. all: 37400 / Num. obs: 37400 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 25.26 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 8.29 / Num. unique all: 3491 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLM Resolution: 1.52→26.33 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 699172.65 / 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: 39.8092 Å2 / ksol: 0.366753 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.52→26.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.57 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
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Xplor file |
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