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Yorodumi- PDB-4l13: Crystal structure of Ligand Free EGFP-based Calcium Sensor CatchER -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l13 | ||||||
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Title | Crystal structure of Ligand Free EGFP-based Calcium Sensor CatchER | ||||||
Components | EGFP-based Calcium Sensor CatchER | ||||||
Keywords | CALCIUM BINDING PROTEIN / chromophore / luminescence / fluorescent protein / calcium sensor / metal ions / gadolinium | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Zhang, Y. / Weber, I.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural basis for a hand-like site in the calcium sensor CatchER with fast kinetics. Authors: Zhang, Y. / Reddish, F. / Tang, S. / Zhuo, Y. / Wang, Y.F. / Yang, J.J. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l13.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l13.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 4l13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l13_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 4l13_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 4l13_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4l13_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/4l13 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/4l13 | HTTPS FTP |
-Related structure data
Related structure data | 4l12C 4l1iC 2okwS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26141.316 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Mutation: F64L, S65T, S147E, M153T, V163A, S202D, Q204E, F223E, T225E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212 |
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#2: Chemical | ChemComp-ACY / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUE SER 65 UNDERWENT MUTATION TO THR 65. THR 65, TYR 66, AND GLY 67 CIRCULARIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 51 mM HEPES, pH 7.0, 1 mM beta-mercaptoethanol, 50 mM sodium acetate, 17% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2010 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. all: 38048 / Num. obs: 38048 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 7.7 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OKW Resolution: 1.66→31.08 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.826 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→31.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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