[English] 日本語
Yorodumi- PDB-1aux: STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aux | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND | ||||||
Components | SYNAPSIN IA | ||||||
Keywords | TRANSFERASE / SYNAPSE / PHOSPHORYLATION / SYNAPSIN IA C-DOMAIN / ATP-BINDING | ||||||
Function / homology | Function and homology information neurotransmitter secretion / cell projection / synaptic vesicle membrane / synaptic vesicle / actin binding / Golgi apparatus / ATP binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Esser, L. / Wang, C. / Deisenhofer, J. | ||||||
Citation | Journal: EMBO J. / Year: 1998 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: Journal: Protein Sci. / Year: 1997 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: Journal: Science / Year: 1989 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1aux.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1aux.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 1aux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/1aux ftp://data.pdbj.org/pub/pdb/validation_reports/au/1aux | HTTPS FTP |
---|
-Related structure data
Related structure data | 1auvSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.445, -0.317, 0.8375), Vector: |
-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.) Bos taurus (cattle) / Plasmid: PSYB21 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P17599 #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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 140 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
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: 1.5418 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|