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Yorodumi- PDB-6j7h: Crystal structure of blue fluorescent protein from metagenomic library -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j7h | ||||||
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Title | Crystal structure of blue fluorescent protein from metagenomic library | ||||||
Components | Blue fluorescent protein | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / BFP | ||||||
Function / homology | Function and homology information 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity Similarity search - Function | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.309 Å | ||||||
Authors | Seo, P.W. / Kim, J.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Structure-Guided Generation of a Redox-Independent Blue Fluorescent Protein from mBFP. Authors: Seo, P.W. / Jo, E.S. / You, S.H. / Cheong, D.E. / Kim, G.J. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j7h.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j7h.ent.gz | 149.5 KB | Display | PDB format |
PDBx/mmJSON format | 6j7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j7h_validation.pdf.gz | 458.9 KB | Display | wwPDB validaton report |
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Full document | 6j7h_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 6j7h_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 6j7h_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/6j7h ftp://data.pdbj.org/pub/pdb/validation_reports/j7/6j7h | HTTPS FTP |
-Related structure data
Related structure data | 6j7uC 3v2gS S: Starting model for refinement C: citing same article (ref.) |
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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: 26882.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: D6NKF4, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) #2: 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: 2.03 Å3/Da / Density % sol: 39.49 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M BICINE pH 9.0, 0.3M Magnesium nitrate, 22% w/v PEG 2000, 4% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 39207 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rpim(I) all: 0.088 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Num. unique obs: 1928 / Rpim(I) all: 0.327 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V2G Resolution: 2.309→48.347 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.309→48.347 Å
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Refine LS restraints |
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LS refinement shell |
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