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Yorodumi- PDB-2c5i: N-terminal domain of tlg1 complexed with N-terminus of vps51 in d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c5i | ||||||
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Title | N-terminal domain of tlg1 complexed with N-terminus of vps51 in distorted conformation | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / PROTEIN TRANSPORT-COMPLEX / SNARE / VFT COMPLEX / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information GARP complex / Retrograde transport at the Trans-Golgi-Network / budding cell apical bud growth / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus / intracellular sphingolipid homeostasis / Golgi to endosome transport / vesicle organization / vesicle fusion / vesicle docking ...GARP complex / Retrograde transport at the Trans-Golgi-Network / budding cell apical bud growth / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus / intracellular sphingolipid homeostasis / Golgi to endosome transport / vesicle organization / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / protein targeting to vacuole / retrograde transport, endosome to Golgi / regulation of cell size / positive regulation of macroautophagy / endomembrane system / SNARE binding / intracellular protein transport / trans-Golgi network / endocytosis / protein transport / late endosome membrane / early endosome membrane / endosome membrane / endosome / Golgi membrane / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Fridmann-Sirkis, Y. / Kent, H.M. / Lewis, M.J. / Evans, P.R. / Pelham, H.R.B. | ||||||
Citation | Journal: Traffic / Year: 2006 Title: Structural Analysis of the Interaction between the Snare Tlg1 and Vps51. Authors: Fridmann-Sirkis, Y. / Kent, H.M. / Lewis, M.J. / Evans, P.R. / Pelham, H.R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c5i.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c5i.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 2c5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/2c5i ftp://data.pdbj.org/pub/pdb/validation_reports/c5/2c5i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3523.099 Da / Num. of mol.: 1 / Fragment: N-TERMINAL, RESIDUES 2-30 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P36116 |
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#2: Protein | Mass: 12012.843 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q03322 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 5.5 Details: 8 MG/ML PROTEIN, 66% SATURATED AMMONIUM SULPHATE, 100 MM NA CITRATE PH 5.5 WITH A 3-FOLD MOLAR EXCESS OF THE PEPTIDE, 20% GLYCEROL FOR FREEZING |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939,0.981 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 14, 2004 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→41 Å / Num. obs: 7108 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 21 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 24 | |||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 22 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→56.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.559 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.269 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→56.8 Å
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Refine LS restraints |
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