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Yorodumi- PDB-6o62: Crystal structure of Sec4p, a Rab family GTPase from Candida albicans -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o62 | ||||||
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Title | Crystal structure of Sec4p, a Rab family GTPase from Candida albicans | ||||||
Components | Ras-related protein SEC4 | ||||||
Keywords | PROTEIN BINDING / G-PROTEIN / RAB / GDP / P-LOOP / GTPASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID | ||||||
Function / homology | Function and homology information spitzenkorper / cellular response to xenobiotic stimulus => GO:0071466 / vesicle targeting / incipient cellular bud site / vesicle fusion / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / regulation of exocytosis / transport vesicle membrane ...spitzenkorper / cellular response to xenobiotic stimulus => GO:0071466 / vesicle targeting / incipient cellular bud site / vesicle fusion / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / regulation of exocytosis / transport vesicle membrane / exocytosis / protein secretion / protein localization to plasma membrane / extracellular vesicle / endosome / GTPase activity / GTP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Stogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: To be published Authors: Stogios, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o62.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o62.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/6o62 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/6o62 | HTTPS FTP |
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-Related structure data
Related structure data | 1z0aS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20824.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 Gene: SEC4, CAALFM_CR01750CA, Ca49C4.03c, CaO19.10103, CaO19.2571 Plasmid: pMCSG68SBPTEV Production host: Escherichia coli BL21(DE3)-Magic (bacteria) Strain (production host): BL21(DE3)-Magic / References: UniProt: P0CY31 |
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#2: Chemical | ChemComp-GDP / |
#3: 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: 1.83 Å3/Da / Density % sol: 32.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Ammonium phosphate dibasic 2.4M, Tris 0.1M pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→25 Å / Num. obs: 11798 / % possible obs: 94.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.62 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 3 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 515 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z0A Resolution: 1.88→24.04 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→24.04 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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