+Open data
-Basic information
Entry | Database: PDB / ID: 4z8y | ||||||
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Title | Crystal structure of Rab GTPase Sec4p mutant - S29V | ||||||
Components | Ras-related protein SEC4 | ||||||
Keywords | GTP binding protein / GTPase / GDP bound / Rab | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rinadi, F.C. / Collins, R.N. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2015 Title: New insights into the molecular mechanism of the Rab GTPase Sec4p activation. Authors: Rinaldi, F.C. / Packer, M. / Collins, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z8y.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z8y.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 4z8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z8y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4z8y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4z8y_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 4z8y_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/4z8y ftp://data.pdbj.org/pub/pdb/validation_reports/z8/4z8y | HTTPS FTP |
-Related structure data
Related structure data | 4zdwC 1g16S 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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Unit cell |
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-Components
#1: Protein | Mass: 19134.889 Da / Num. of mol.: 2 / Mutation: S29V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SEC4, SRO6, YFL005W / Plasmid: ppSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07560 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.72 % |
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Crystal grow | Temperature: 293.15 K / Method: batch mode Details: After initial crystal screening, small crystals were obtained in 14% PEG3350, 200mM Zinc Acetate. After refinement, large single crystals were obtained in 14% PEG4000, 50mM Zinc Acetate. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen gas stream |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→66.2 Å / Num. obs: 23244 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.87→2 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G16 Resolution: 1.9→28.3 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.456 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.259 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.195 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→28.3 Å
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