+Open data
-Basic information
Entry | Database: PDB / ID: 6van | ||||||
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Title | Crystal structure of caltubin from the great pond snail | ||||||
Components | Caltubin, EF-hand | ||||||
Keywords | METAL BINDING PROTEIN / EF-hand / calcium-binding protein / invertebrate / Structural Genomics Consortium / SGC | ||||||
Function / homology | EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / STRONTIUM ION / Calcium-binding protein Function and homology information | ||||||
Biological species | Lymnaea stagnalis (great pond snail) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.33 Å | ||||||
Authors | Dong, A. / Li, A. / Zhang, Q. / Barszczyk, A. / Chern, Y.H. / Arrowsmith, C.H. / Edwards, A.M. / Zhong, Z.P. / Tong, Y. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Canada, 1items
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Citation | Journal: to be published Title: Cell-penetrating caltubin promotes neurite outgrowth and regrowth through calcium-dependent microtubule regulation Authors: Dong, A. / Li, A. / Zhang, Q. / Barszczyk, A. / Chern, Y.H. / Arrowsmith, C.H. / Edwards, A.M. / Zhong, Z.P. / Tong, Y. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6van.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6van.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 6van.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6van_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 6van_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 6van_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6van_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/6van ftp://data.pdbj.org/pub/pdb/validation_reports/va/6van | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16471.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pET28-MKH8SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pRARE2 / References: UniProt: Q2VA57 #2: Chemical | ChemComp-SR / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.99 Å3/Da / Density % sol: 38.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 24% PEG 3350, 0.1M Tris pH7.5, 150 mM SrCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 1, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.33→50 Å / Num. obs: 58175 / % possible obs: 97.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.031 / Rrim(I) all: 0.063 / Χ2: 0.934 / Net I/σ(I): 8.6 / Num. measured all: 232691 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.33→45.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.08 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 71.44 Å2 / Biso mean: 17.401 Å2 / Biso min: 7.59 Å2
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Refinement step | Cycle: final / Resolution: 1.33→45.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.33→1.365 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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