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Yorodumi- PDB-5ca9: Structures of the candida albicans sey1p GTPase in complex with G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ca9 | ||||||||||||
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Title | Structures of the candida albicans sey1p GTPase in complex with GDPAlF4- | ||||||||||||
Components | Protein SEY1 | ||||||||||||
Keywords | HYDROLASE / ER / Sey1p / membrance fusion / dynamin | ||||||||||||
Function / homology | Function and homology information endoplasmic reticulum inheritance / hexose transmembrane transport / endoplasmic reticulum membrane fusion / cortical endoplasmic reticulum / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum Similarity search - Function | ||||||||||||
Biological species | Candida albicans (yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||||||||
Authors | Yan, L. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J.Cell Biol. / Year: 2015 Title: Structures of the yeast dynamin-like GTPase Sey1p provide insight into homotypic ER fusion Authors: Yan, L. / Sun, S. / Wang, W. / Shi, J. / Hu, X. / Wang, S. / Su, D. / Rao, Z. / Hu, J. / Lou, Z. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ca9.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ca9.ent.gz | 233 KB | Display | PDB format |
PDBx/mmJSON format | 5ca9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ca9_validation.pdf.gz | 828.2 KB | Display | wwPDB validaton report |
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Full document | 5ca9_full_validation.pdf.gz | 872.1 KB | Display | |
Data in XML | 5ca9_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 5ca9_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/5ca9 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/5ca9 | 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: 79124.000 Da / Num. of mol.: 1 / Fragment: UNP residues 1-692 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: SEY1, NAG6, CaO19.2151, CaO19.9698 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C0L9, dynamin GTPase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ALF / |
#4: Chemical | ChemComp-GDP / |
#5: Water | ChemComp-HOH / |
Sequence details | 1. SEQUENCE CONFLICTS D270G, A337T AND I479V ARE BASED ON BAB43823.1 ACCORDING TO DATABASE Q9C0L9 ...1. SEQUENCE CONFLICTS D270G, A337T AND I479V ARE BASED ON BAB43823.1 ACCORDING TO DATABASE Q9C0L9 (SEY1_CANAL). 2. THE CODON CUG (MRNA CUG CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 289 K / Method: evaporation Details: 160 mM Lithium sulfate monohydrate, 80 mM Tris pH 8.5, 20% w/v Polyethylene glycol 3,350, 40 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate pH 5.6, 6% w/v Polyethylene glycol ...Details: 160 mM Lithium sulfate monohydrate, 80 mM Tris pH 8.5, 20% w/v Polyethylene glycol 3,350, 40 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate pH 5.6, 6% w/v Polyethylene glycol 4,000, 20 mM spermidine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 21774 / % possible obs: 99 % / Redundancy: 10.28 % / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 2.8→2.85 Å |
-Processing
Software |
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Refinement | Resolution: 2.8→48.76 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.112 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / 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: 78.318 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→48.76 Å
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Refine LS restraints |
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