+Open data
-Basic information
Entry | Database: PDB / ID: 1g16 | ||||||
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Title | CRYSTAL STRUCTURE OF SEC4-GDP | ||||||
Components | RAS-RELATED PROTEIN SEC4 | ||||||
Keywords | SIGNALING PROTEIN / ENDOCYTOSIS/EXOCYTOSIS / G protein Rab / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information ascospore-type prospore assembly / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / transport vesicle membrane ...ascospore-type prospore assembly / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / transport vesicle membrane / exocytosis / protein secretion / transport vesicle / Neutrophil degranulation / autophagy / vesicle / mitochondrial outer membrane / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / plasma membrane Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Stroupe, C. / Brunger, A.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of a Rab protein in its inactive and active conformations. Authors: Stroupe, C. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g16.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g16.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g16_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1g16_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1g16_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 1g16_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/1g16 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/1g16 | HTTPS FTP |
-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 | Mass: 19305.557 Da / Num. of mol.: 4 / Fragment: RESIDUES 18-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07560 #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-GDP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.07 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: microbatch / pH: 5.7 Details: PEG 4000, 12% Cobalt Chloride, 70 mM Sodium cacodylate, pH 5.7, microbatch, temperature 21K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→28.9 Å / Num. all: 117032 / Num. obs: 104861 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.89 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20 | |||||||||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.258 / Num. unique all: 11775 / % possible all: 60.8 | |||||||||||||||||||||
Reflection | *PLUS Num. measured all: 408214 | |||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 60.8 % / Mean I/σ(I) obs: 5.2 |
-Processing
Software |
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Refinement | Resolution: 1.8→28.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1170816.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.58 Å2 / ksol: 0.384 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→28.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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