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Yorodumi- PDB-7vsx: Crystal structure of QL-nanoKAZ (Reverse mutant of nanoKAZ with L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vsx | ||||||
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Title | Crystal structure of QL-nanoKAZ (Reverse mutant of nanoKAZ with L18Q and V27L) | ||||||
Components | QLnK | ||||||
Keywords | LUMINESCENT PROTEIN / mutated 19 kDa protein / Oplophorus luciferase | ||||||
Biological species | Oplophorus gracilirostris (crustacean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.698 Å | ||||||
Authors | Tomabechi, Y. / Sekine, S. / Shirouzu, M. / Takamitsu, H. / Satoshi, I. | ||||||
Funding support | 1items
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Citation | Journal: Plos One / Year: 2022 Title: Reverse mutants of the catalytic 19 kDa mutant protein (nanoKAZ/nanoLuc) from Oplophorus luciferase with coelenterazine as preferred substrate. Authors: Inouye, S. / Sato, J.I. / Sahara-Miura, Y. / Tomabechi, Y. / Sumida, Y. / Sekine, S.I. / Shirouzu, M. / Hosoya, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vsx.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vsx.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vsx_validation.pdf.gz | 714.6 KB | Display | wwPDB validaton report |
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Full document | 7vsx_full_validation.pdf.gz | 715.7 KB | Display | |
Data in XML | 7vsx_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 7vsx_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/7vsx ftp://data.pdbj.org/pub/pdb/validation_reports/vs/7vsx | HTTPS FTP |
-Related structure data
Related structure data | 5b0uS S: Starting model for refinement |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19187.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-MES / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES (pH6.5) 1.8-1.9 M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Nov 18, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.698→47.482 Å / Num. obs: 26866 / % possible obs: 99.7 % / Redundancy: 7.319 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Χ2: 0.976 / Net I/σ(I): 15.08 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B0U Resolution: 1.698→47.482 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.32 Å2 / Biso mean: 37.6905 Å2 / Biso min: 19.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.698→47.482 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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