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Open data
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Basic information
Entry | Database: PDB / ID: 4npk | ||||||
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Title | Extended-Synaptotagmin 2, C2A- and C2B-domains, calcium bound | ||||||
![]() | Extended synaptotagmin-2 | ||||||
![]() | MEMBRANE PROTEIN / CALCIUM/PHOSPHOLIPID BINDING PROTEIN / C2 domain / ER to plasma membrane / membrane traffic / protein targeting / Plasma membrane | ||||||
Function / homology | ![]() endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / Glycosphingolipid transport / phosphatidylcholine binding / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / lipid transport / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol binding ...endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / Glycosphingolipid transport / phosphatidylcholine binding / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / lipid transport / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol binding / cytoplasmic side of plasma membrane / endocytosis / cadherin binding / calcium ion binding / endoplasmic reticulum membrane / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomchick, D.R. / Rizo, J. / Xu, J. | ||||||
![]() | ![]() Title: Structure and ca(2+)-binding properties of the tandem c2 domains of e-syt2. Authors: Xu, J. / Bacaj, T. / Zhou, A. / Tomchick, D.R. / Sudhof, T.C. / Rizo, J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: E-Syts, a family of membranous Ca2+-sensor proteins with multiple C2 domains. Authors: Min, S.W. / Chang, W.P. / Sudhof, T.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.3 KB | Display | ![]() |
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PDB format | ![]() | 141.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.6 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4npjSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34265.121 Da / Num. of mol.: 1 / Fragment: C2A and C2B domains / Mutation: A512V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 6% PEG 8000, 0.1 M Hepes pH 8.0, 0.125 M NaCl, 2.5% glycerol, 0.02 M CaCl2, 0.5 mM TCEP, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012 / Details: monochromator |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 12318 / Num. obs: 12318 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 68.45 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.45 / Num. unique all: 263 / % possible all: 38 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 4NPJ Resolution: 2.552→28.986 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 42.82 / Stereochemistry target values: ML Details: Used reference model restraints. Reference model was
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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 max: 275.75 Å2 / Biso mean: 133.5576 Å2 / Biso min: 69.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a free: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.552→28.986 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: 4
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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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