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Yorodumi- PDB-4kgf: Crystal structure of near-infrared fluorescent protein with an ex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kgf | ||||||
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Title | Crystal structure of near-infrared fluorescent protein with an extended stokes shift, ph 8.0 | ||||||
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 | 4kgf.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kgf.ent.gz | 160.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kgf_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 4kgf_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 4kgf_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 4kgf_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/4kgf ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kgf | HTTPS FTP |
-Related structure data
Related structure data | 4kgeSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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 | ChemComp-CL / | #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: 3.17 Å3/Da / Density % sol: 61.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Na-acetate, pH 4.5, 3.0M NaCl. Then Solution slowly replaced with 0.1M Tris-HCl, pH 8.0, 3.0M NaCl 8-10 min, color change (darker), 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 22, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SAD / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.23→50 Å / Num. obs: 35919 / % possible obs: 99.2 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.074 / Χ2: 1.302 / Net I/σ(I): 11.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4KGE Resolution: 2.3→46.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.491 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.04 / 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: 150.45 Å2 / Biso mean: 56.2677 Å2 / Biso min: 25.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→46.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 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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