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Yorodumi- PDB-4kge: Crystal structure of near-infrared fluorescent protein with an ex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kge | ||||||
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Title | Crystal structure of near-infrared fluorescent protein with an extended stokes shift, pH 4.5 | ||||||
Components | TagRFP675, red fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / STRUCTURAL GENOMICS / PROTEINSTRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCHCONSORTIUM / HYDROLASE / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Malashkevich, V.N. / Piatkevich, K. / Almo, S.C. / Verkhusha, V. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: Sci Rep / Year: 2013 Title: Extended Stokes shift in fluorescent proteins: chromophore-protein interactions in a near-infrared TagRFP675 variant. Authors: Piatkevich, K.D. / Malashkevich, V.N. / Morozova, K.S. / Nemkovich, N.A. / Almo, S.C. / Verkhusha, V.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kge.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kge.ent.gz | 160.2 KB | Display | PDB format |
PDBx/mmJSON format | 4kge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/4kge ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kge | HTTPS FTP |
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-Related structure data
Related structure data | 4kgfC 3bxaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | dimeric |
-Components
#1: Protein | Mass: 27797.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: PBAD/HIS-B / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 #2: Chemical | #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: 3.2 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M Na-acetate, pH 4.5, 3.0M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SAD / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 32982 / % possible obs: 99.5 % / Redundancy: 21 % / Rmerge(I) obs: 0.09 / Χ2: 1.007 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 45.23 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BXA Resolution: 2.3→47.11 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2287 / WRfactor Rwork: 0.1842 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8617 / SU B: 7.799 / SU ML: 0.105 / SU R Cruickshank DPI: 0.0466 / SU Rfree: 0.0408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 133.06 Å2 / Biso mean: 40.5447 Å2 / Biso min: 17.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.303→2.362 Å / Total num. of bins used: 20
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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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