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Yorodumi- PDB-3a6q: E13T mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a6q | ||||||
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Title | E13T mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) | ||||||
Components | FMN-binding protein | ||||||
Keywords | ELECTRON TRANSPORT / Flavoprotein / FMN / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Nakanishi, T. / Haruyama, Y. / Inoue, H. / Kitamura, M. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2010 Title: Effects of the disappearance of one charge on ultrafast fluorescence dynamics of the FMN binding protein. Authors: Chosrowjan, H. / Taniguchi, S. / Mataga, N. / Nakanishi, T. / Haruyama, Y. / Sato, S. / Kitamura, M. / Tanaka, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a6q.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a6q.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 3a6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a6q_validation.pdf.gz | 1007.7 KB | Display | wwPDB validaton report |
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Full document | 3a6q_full_validation.pdf.gz | 1008.6 KB | Display | |
Data in XML | 3a6q_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3a6q_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/3a6q ftp://data.pdbj.org/pub/pdb/validation_reports/a6/3a6q | HTTPS FTP |
-Related structure data
Related structure data | 3a6rC 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: 13125.057 Da / Num. of mol.: 2 / Mutation: E13T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / Gene: DvMF_2023 / Plasmid: PMKBT-1001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46604 #2: Chemical | #3: Chemical | #4: 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: 2.4 Å3/Da / Density % sol: 48.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 10% 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-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 3, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 48510 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FLM Resolution: 1.4→10 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.694 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: REFINED INDIVIDUALLY
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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: 10.813 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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