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Yorodumi- PDB-3qof: Crystal structure of the cytosolic domain of human atlastin-1 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qof | ||||||
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Title | Crystal structure of the cytosolic domain of human atlastin-1 in complex with GDP, orthorhombic form | ||||||
Components | Atlastin-1 | ||||||
Keywords | HYDROLASE / GTPase / homotypic fusion / fusion of ER membranes / GDP / GTP / endoplasmic reticulum | ||||||
Function / homology | Function and homology information endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon ...endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å | ||||||
Authors | Liu, X. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structures of the atlastin GTPase provide insight into homotypic fusion of endoplasmic reticulum membranes. Authors: Bian, X. / Klemm, R.W. / Liu, T.Y. / Zhang, M. / Sun, S. / Sui, X. / Liu, X. / Rapoport, T.A. / Hu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qof.cif.gz | 329.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qof.ent.gz | 259.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qof_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3qof_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3qof_validation.xml.gz | 66 KB | Display | |
Data in CIF | 3qof_validation.cif.gz | 87.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qof ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qof | HTTPS FTP |
-Related structure data
Related structure data | 3qnuSC 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: 52718.609 Da / Num. of mol.: 4 / Fragment: atlastin ecto-domain (UNP RESIDUES 18-447) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Plasmid: pet30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8WXF7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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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: 2.92 Å3/Da / Density % sol: 57.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.1M Tris-HCl, pH8.3, 25%(w/v) PEG 3350, 0.1M (NH4)2HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 14, 2010 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→48.751 Å / Num. all: 61398 / Num. obs: 60656 / % possible obs: 98.79 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QNU Resolution: 2.802→40 Å / SU ML: 0.4 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 1 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.413 Å2 / ksol: 0.302 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.802→40 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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