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Yorodumi- PDB-6mas: X-ray Structure of Branchiostoma floridae fluorescent protein lanFP10G -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mas | |||||||||
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Title | X-ray Structure of Branchiostoma floridae fluorescent protein lanFP10G | |||||||||
Components | Uncharacterized protein | |||||||||
Keywords | FLUORESCENT PROTEIN / Gly-Tyr-Gly chromophore | |||||||||
Function / homology | Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Green fluorescent protein Function and homology information | |||||||||
Biological species | Branchiostoma floridae (Florida lancelet) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Muslinkina, L. / Pletneva, N. / Pletnev, V. / Pletnev, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Mol. Biol. / Year: 2019 Title: Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue. Authors: Muslinkina, L. / Roldan-Salgado, A. / Gaytan, P. / Juarez-Gonzalez, V.R. / Rudino, E. / Pletneva, N. / Pletnev, V. / Dauter, Z. / Pletnev, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mas.cif.gz | 826.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mas.ent.gz | 687.6 KB | Display | PDB format |
PDBx/mmJSON format | 6mas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/6mas ftp://data.pdbj.org/pub/pdb/validation_reports/ma/6mas | HTTPS FTP |
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-Related structure data
Related structure data | 6m9xC 6m9yC 6m9zC 4hvfS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25938.270 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Branchiostoma floridae (Florida lancelet) Gene: BRAFLDRAFT_75522 / Production host: Escherichia coli (E. coli) / References: UniProt: C3YRA2 #2: Chemical | ChemComp-GOL / #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: 2.26 Å3/Da / Density % sol: 45.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Imidazole pH 7.0, 20% PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2018 / Details: m | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→30 Å / Num. obs: 451144 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.035 / Rrim(I) all: 0.069 / Χ2: 0.879 / Net I/σ(I): 8.5 / Num. measured all: 1703469 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HVF Resolution: 1.3→29.82 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1474 / WRfactor Rwork: 0.1197 / FOM work R set: 0.9017 / SU B: 1.446 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0383 / SU Rfree: 0.0378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.23 Å2 / Biso mean: 15.252 Å2 / Biso min: 2.84 Å2
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Refinement step | Cycle: final / Resolution: 1.3→29.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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