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- PDB-1aux: STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1aux | ||||||
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Title | STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND | ||||||
![]() | SYNAPSIN IA | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() neurotransmitter secretion / cell projection / synaptic vesicle membrane / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Esser, L. / Wang, C. / Deisenhofer, J. | ||||||
![]() | ![]() 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. #1: ![]() Title: Identification, Expression, and Crystallization of the Protease-Resistant Conserved Domain of Synapsin I Authors: Wang, C.R. / Esser, L. / Smagula, C.S. / Sudhof, T.C. / Deisenhofer, J. #2: ![]() Title: Synapsins: Mosaics of Shared and Individual Domains in a Family of Synaptic Vesicle Phosphoproteins Authors: Sudhof, T.C. / Czernik, A.J. / Kao, H.T. / Takei, K. / Johnston, P.A. / Horiuchi, A. / Kanazir, S.D. / Wagner, M.A. / Perin, M.S. / De Camilli, P. / Greengard, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.2 KB | Display | ![]() |
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PDB format | ![]() | 101.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1auvSC 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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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.445, -0.317, 0.8375), Vector ![]() |
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Components
#1: Protein | Mass: 34901.980 Da / Num. of mol.: 2 / Fragment: C DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | ![]() Nonpolymer details | ONE CALCIUM ION AND ONE MOLECULE OF ADENOSINE DIPHOSPHATE MONOTHIOPHOSPHATE (ATP-GAMMA-S) ARE BOUND ...ONE CALCIUM ION AND ONE MOLECULE OF ADENOSINE DIPHOSPHAT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % | ||||||||||||||||||||||||
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Crystal grow![]() | pH: 7.25 Details: PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 100 MM HEPES, PH 7.25, THEN DIRECTLY TRANSFERRED TO 30 % PEG 4000, 50 MM HEPES, PH 7.5, 50 MM NACL. AFTER 12 H, CRYSTALS WERE TRANSFERRED TO 30 % ...Details: PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 100 MM HEPES, PH 7.25, THEN DIRECTLY TRANSFERRED TO 30 % PEG 4000, 50 MM HEPES, PH 7.5, 50 MM NACL. AFTER 12 H, CRYSTALS WERE TRANSFERRED TO 30 % PEG, 75 MM HEPES, PH 7.5, 75 MM NACL, 2.5 MM CACL2, 2.5 MM ATP-GAMMA-S FOR 23 H. | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Wang, C.R., (1997) Protein Sci., 6, 2264. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→20 Å / Num. obs: 28177 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 1.44 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.21 / % possible all: 71.7 |
Reflection | *PLUS Num. measured all: 88952 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1AUV Resolution: 2.3→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 53.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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