+Open data
-Basic information
Entry | Database: PDB / ID: 1cr5 | ||||||
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Title | N-TERMINAL DOMAIN OF SEC18P | ||||||
Components | SEC18P (RESIDUES 22 - 210) | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / DOUBLE-PSI BETA BARREL / VESICLE FUSION / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information inter-Golgi cisterna vesicle-mediated transport / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / SNARE complex disassembly / vesicle fusion with Golgi apparatus / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / vacuole fusion, non-autophagic / COPII-mediated vesicle transport / intra-Golgi vesicle-mediated transport ...inter-Golgi cisterna vesicle-mediated transport / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / SNARE complex disassembly / vesicle fusion with Golgi apparatus / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / vacuole fusion, non-autophagic / COPII-mediated vesicle transport / intra-Golgi vesicle-mediated transport / phosphatidic acid binding / Golgi to plasma membrane protein transport / Golgi stack / mating projection tip / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / SNARE binding / macroautophagy / Golgi apparatus / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Babor, S.M. / Fass, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Crystal structure of the Sec18p N-terminal domain. Authors: Babor, S.M. / Fass, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cr5.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cr5.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cr5_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 1cr5_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 1cr5_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 1cr5_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/1cr5 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/1cr5 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 21323.959 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / References: UniProt: P18759 #2: Chemical | ChemComp-NEN / #3: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 1.96 Å3/Da / Density % sol: 37.18 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 9, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 22632 / Num. obs: 22366 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Redundancy: 4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.115 / Num. unique all: 2200 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 176811 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Resolution: 2.3→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |