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Yorodumi- PDB-1l4a: X-RAY STRUCTURE OF THE NEURONAL COMPLEXIN/SNARE COMPLEX FROM THE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l4a | ||||||
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Title | X-RAY STRUCTURE OF THE NEURONAL COMPLEXIN/SNARE COMPLEX FROM THE SQUID LOLIGO PEALEI | ||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / SNARE / SNARE complex / membrane fusion / neurotransmission / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information SNAP receptor activity / neurotransmitter transport / syntaxin binding / exocytosis / vesicle-mediated transport / intracellular protein transport / synaptic vesicle membrane / membrane => GO:0016020 / neuron projection / synapse ...SNAP receptor activity / neurotransmitter transport / syntaxin binding / exocytosis / vesicle-mediated transport / intracellular protein transport / synaptic vesicle membrane / membrane => GO:0016020 / neuron projection / synapse / membrane / cytosol Similarity search - Function | ||||||
Biological species | Loligo pealei (longfin inshore squid) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Bracher, A. / Kadlec, J. / Betz, H. / Weissenhorn, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: X-ray structure of a neuronal complexin-SNARE complex from squid. Authors: Bracher, A. / Kadlec, J. / Betz, H. / Weissenhorn, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l4a.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l4a.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 1l4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/1l4a ftp://data.pdbj.org/pub/pdb/validation_reports/l4/1l4a | HTTPS FTP |
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-Related structure data
Related structure data | 1sfcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains the biologically relevant structure |
-Components
-Protein , 3 types, 3 molecules ABE
#1: Protein | Mass: 9046.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pRSet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: P47194 |
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#2: Protein | Mass: 9981.440 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pMal-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: O46345 |
#5: Protein | Mass: 9251.200 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pMal-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: Q95PA1 |
-S-SNAP25 fusion ... , 2 types, 2 molecules CD
#3: Protein | Mass: 9566.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pRSet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: Q8T3S4 |
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#4: Protein | Mass: 9671.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pRSet / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: Q8T3S4 |
-Non-polymers , 1 types, 23 molecules
#6: Water | ChemComp-HOH / |
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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: 2.55 Å3/Da / Density % sol: 51.3 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 5% MPD, 7.5% PEG550-MME, 20MM beta mercaptoethanol, 20MM Tris PH 7.2, 50MM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.915 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→15 Å / Num. all: 10799 / Num. obs: 10128 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 79.04 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.95→3.13 Å / Redundancy: 4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.1 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 75 Å / Num. measured all: 41657 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 93 % / Rmerge(I) obs: 0.219 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SFC Resolution: 2.95→15 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.2327 Å2 / ksol: 0.26842 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.13 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 15 Å / Rfactor all: 0.3004 / Rfactor Rfree: 0.3445 / Rfactor Rwork: 0.297 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.397 / Rfactor Rwork: 0.346 |