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- PDB-1px2: Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1px2 | ||||||
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Title | Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP (Form 1) | ||||||
![]() | Synapsin I | ||||||
![]() | MEMBRANE PROTEIN / ATP binding / ATP grasp / calcium (II) ion | ||||||
Function / homology | ![]() synaptic vesicle cycle / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / synaptic vesicle clustering / extrinsic component of synaptic vesicle membrane / regulation of synaptic vesicle cycle / synaptonemal complex / neurotransmitter secretion / regulation of synaptic vesicle exocytosis / presynaptic active zone ...synaptic vesicle cycle / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / synaptic vesicle clustering / extrinsic component of synaptic vesicle membrane / regulation of synaptic vesicle cycle / synaptonemal complex / neurotransmitter secretion / regulation of synaptic vesicle exocytosis / presynaptic active zone / neuron development / synapse organization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / presynapse / actin binding / cell body / postsynaptic density / cytoskeleton / axon / synapse / dendrite / protein kinase binding / Golgi apparatus / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brautigam, C.A. / Chelliah, Y. / Deisenhofer, J. | ||||||
![]() | ![]() Title: Tetramerization and ATP binding by a protein comprising the A, B, and C domains of rat synapsin I. Authors: Brautigam, C.A. / Chelliah, Y. / Deisenhofer, J. #1: ![]() Title: Synapsin I is structurally similar to ATP-utilizing enzymes Authors: Esser, L. / Wang, C.R. / Hosaka, M. / Smagula, C.S. / Sudhof, T.C. / Deisenhofer, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.6 KB | Display | ![]() |
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PDB format | ![]() | 110.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pk8C ![]() 1auxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second half of the (presumably) biological tetramer is generated by the twofold axis: -y + 1, -x + 1, -z + 1/6 |
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Components
#1: Protein | Mass: 45539.398 Da / Num. of mol.: 2 / Fragment: A, B, & C domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.89 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEGMME 5K, Tris, NaCl, Ca.ATP, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2000 |
Radiation | Monochromator: Horizontally bent Si(111), with monochromatic mirrors of Rh-coated Si Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.942 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→40 Å / Num. all: 41721 / Num. obs: 41721 / % possible obs: 99.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 28.5 Å2 / Rsym value: 0.082 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.23→2.31 Å / Redundancy: 9 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 4060 / Rsym value: 0.391 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 40542 / Num. measured all: 467389 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.391 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AUX, Ca and ATP-gamma-S removed Resolution: 2.23→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: modified Engh & Huber Details: Although the A, B, and C domains of rat synapsin I were included in crystallization, only the C domain was observed. Some residues have side chains that are set to occupancies of 0.00 due to disorder.
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Solvent computation | Solvent model: flat model / Bsol: 40.9992 Å2 / ksol: 0.326988 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.23→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.37 Å / Rfactor Rfree error: 0.017
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.24 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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