[English] 日本語
Yorodumi- PDB-4ndb: X-ray structure of a mutant (T61D) of calexcitin - a neuronal cal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ndb | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of a mutant (T61D) of calexcitin - a neuronal calcium-signalling protein | ||||||
Components | Calexcitin | ||||||
Keywords | SIGNALING PROTEIN / EF-hand / calcium-binding / neuron | ||||||
Function / homology | EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha / metal ion binding / Calexcitin Function and homology information | ||||||
Biological species | Doryteuthis pealeii (longfin inshore squid) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Erskine, P.T. / Fokas, A. / Muriithi, C. / Razzall, E. / Bowyer, A. / Findlow, I.S. / Werner, J.M. / Wallace, B.A. / Wood, S.P. / Cooper, J.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure-function studies of a neuronal calcium-signalling protein. Authors: Erskine, P.T. / Fokas, A. / Muriithi, C. / Rehman, H. / Yates, L.A. / Bowyer, A. / Findlow, I.S. / Hagan, R. / Werner, J.M. / Miles, A.J. / Wallace, B.A. / Wells, S.A. / Wood, S.P. / Cooper, J.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ndb.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ndb.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 4ndb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/4ndb ftp://data.pdbj.org/pub/pdb/validation_reports/nd/4ndb | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ndcC 4nddC 2ccmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24848.781 Da / Num. of mol.: 2 / Mutation: T61D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Doryteuthis pealeii (longfin inshore squid) Gene: cex / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76764 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 15-40% w/v PEG 4000, 100 mM sodium citrate, 200 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 5.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 3, 2012 |
Radiation | Monochromator: single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.9 Å / Num. all: 30186 / Num. obs: 30186 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.2 / Num. unique all: 4326 / % possible all: 98.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2CCM Resolution: 2→27.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.101 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 30.233 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→27.9 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|