+Open data
-Basic information
Entry | Database: PDB / ID: 5f6t | ||||||
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Title | Structure of calexcitin-Gd3+ complex. | ||||||
Components | Calexcitin | ||||||
Keywords | calcium-binding protein / EF-hand Neuronal calcium signalling | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Doryteuthis pealeii (longfin inshore squid) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å | ||||||
Authors | Chataigner, L. / Guo, J. / Erskine, P.T. / Coker, A.R. / Wood, S.P. / Cooper, J.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Binding of Gd(3+) to the neuronal signalling protein calexcitin identifies an exchangeable Ca(2+)-binding site. Authors: Chataigner, L. / Guo, J. / Erskine, P.T. / Coker, A.R. / Wood, S.P. / Gombos, Z. / Cooper, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f6t.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f6t.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f6t ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f6t | HTTPS FTP |
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-Related structure data
Related structure data | 2ccmS 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
#1: Protein | Mass: 22301.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Doryteuthis pealeii (longfin inshore squid) Gene: cex / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76764 | ||
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#2: Chemical | ChemComp-GD / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 38 % / Description: Plates. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M sodium acetate trihydrate, 0.1 M TRIS pH 8.5, 30 % PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.3 Å / Num. all: 9020 / Num. obs: 9020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 66.2 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 6 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ccm Resolution: 2.201→27.353 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.201→27.353 Å
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Refine LS restraints |
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LS refinement shell |
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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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