+Open data
-Basic information
Entry | Database: PDB / ID: 2c5j | ||||||
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Title | N-terminal domain of tlg1, domain-swapped dimer | ||||||
Components | T-SNARE AFFECTING A LATE GOLGI COMPARTMENT PROTEIN 1 | ||||||
Keywords | PROTEIN TRANSPORT / SNARE / TRANSPORT / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus / Golgi to endosome transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / retrograde transport, endosome to Golgi / endomembrane system ...Retrograde transport at the Trans-Golgi-Network / Golgi vesicle fusion to target membrane / vesicle fusion with Golgi apparatus / Golgi to endosome transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / retrograde transport, endosome to Golgi / endomembrane system / SNARE binding / intracellular protein transport / trans-Golgi network / endocytosis / late endosome membrane / early endosome membrane / endosome membrane / endosome / Golgi membrane / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 2c5j.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c5j.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 2c5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c5j_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
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Full document | 2c5j_full_validation.pdf.gz | 422.5 KB | Display | |
Data in XML | 2c5j_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2c5j_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/2c5j ftp://data.pdbj.org/pub/pdb/validation_reports/c5/2c5j | HTTPS FTP |
-Related structure data
Related structure data | 2c5iSC 2c5kC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 11244.396 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-95 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 #2: 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: 2.9 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | pH: 5.6 Details: 20MG/ML PROTEIN, 8% PEG8000, 80MM K PHOSPHATE PH5.6, FROZEN IN 22.5% GLYCEROL, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 30, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 14293 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.5 / % possible all: 91.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C5I Resolution: 2.1→58.93 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 6.062 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→58.93 Å
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Refine LS restraints |
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