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Yorodumi- PDB-6ir7: Green fluorescent protein variant GFPuv with the modification to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ir7 | |||||||||
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Title | Green fluorescent protein variant GFPuv with the modification to 6-hydroxynorleucine at the C-terminus | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | FLUORESCENT PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.277 Å | |||||||||
Authors | Nakatani, T. / Yasui, N. / Yamashita, A. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Specific modification at the C-terminal lysine residue of the green fluorescent protein variant, GFPuv, expressed in Escherichia coli. Authors: Nakatani, T. / Yasui, N. / Tamura, I. / Yamashita, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ir7.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ir7.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ir7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ir7_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 6ir7_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 6ir7_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 6ir7_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/6ir7 ftp://data.pdbj.org/pub/pdb/validation_reports/ir/6ir7 | HTTPS FTP |
-Related structure data
Related structure data | 6ir6C 1b9cS 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: 26681.920 Da / Num. of mol.: 1 / Mutation: Q80R, F99S, M153T, V163A, A206K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P42212 |
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#2: Chemical | ChemComp-LDO / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
Sequence details | RESIDUE THR 65 HAS BEEN MUTATED TO SER 65. RESIDUES SER 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE THR 65 HAS BEEN MUTATED TO SER 65. RESIDUES SER 65, TYR 66 AND GLY 67 CONSTITUTE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium Sulfate, 0.1 M MES pH 6.5, 30% PEGMME5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→50 Å / Num. obs: 56911 / % possible obs: 96.3 % / Redundancy: 3.1 % / Rsym value: 0.071 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 7.2 / Num. unique obs: 2566 / Rsym value: 0.248 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B9C Resolution: 1.277→47.649 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.24 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.277→47.649 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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