+Open data
-Basic information
Entry | Database: PDB / ID: 4ik4 | ||||||
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Title | High resolution structure of GCaMP3 at pH 5.0 | ||||||
Components | RCaMP, Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / calcium indicator / mutants / fluorescent intensity / dimerization / beta barrel / Calmodulin | ||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / calcium ion binding Similarity search - Function | ||||||
Biological species | Entacmaea quadricolor (sea anemone) Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Chen, Y. / Song, X. / Miao, L. / Zhu, Y. / Ji, G. | ||||||
Citation | Journal: Protein Cell / Year: 2013 Title: Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement. Authors: Chen, Y. / Song, X. / Ye, S. / Miao, L. / Zhu, Y. / Zhang, R.G. / Ji, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ik4.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ik4.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ik4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/4ik4 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/4ik4 | HTTPS FTP |
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-Related 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: 50544.391 Da / Num. of mol.: 1 Mutation: M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T Source method: isolated from a genetically manipulated source Details: CHIMERA OF 10 EXPRESSION TAGS, RESIDUES 11-58 OF RCaMP, LINKER LE, RESIDUES 61-150 OF GREEN FLUORESCENT PROTEIN, LINKER GGTGGSMV, RESIDUES 159-299 OF GREEN FLUORESCENT PROTEIN, RESIDUES 300-448 OF RCaMP Source: (gene. exp.) Entacmaea quadricolor (sea anemone), (gene. exp.) Aequorea victoria (jellyfish) Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: K4DIE3, UniProt: P42212 | ||||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Sequence details | (1) THIS CHIMERA COMPRISES OF 10 EXPRESSION TAGS, RESIDUES 11-58 OF RCaMP, LINKER LE, RESIDUES 61- ...(1) THIS CHIMERA COMPRISES OF 10 EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.67 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Bis-Tris pH 5.0, (NH4)2SO4 and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 2012 |
Radiation | Monochromator: Be filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→22.11 Å / Num. all: 26565 / Num. obs: 26008 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 74.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→22.11 Å / SU ML: 0.25 / σ(F): 0.25 / Phase error: 20.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.688 Å2 / ksol: 0.368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.01→22.11 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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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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