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Yorodumi- PDB-6xjn: Human atlastin-1 (residues 1-439) bound to GDP-Mg2+ exhibits an o... -
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-Basic information
Entry | Database: PDB / ID: 6xjn | ||||||
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Title | Human atlastin-1 (residues 1-439) bound to GDP-Mg2+ exhibits an ordered amino terminus | ||||||
Components | Atlastin-1 | ||||||
Keywords | HYDROLASE / GTPase / fusogen | ||||||
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 / SAD / Resolution: 2.2 Å | ||||||
Authors | O'Donnell, J.P. / Sondermann, H. | ||||||
Citation | Journal: J.Cell Biol. / Year: 2021 Title: The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation. Authors: Kelly, C.M. / Byrnes, L.J. / Neela, N. / Sondermann, H. / O'Donnell, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xjn.cif.gz | 217.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xjn.ent.gz | 146.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xjn_validation.pdf.gz | 911.6 KB | Display | wwPDB validaton report |
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Full document | 6xjn_full_validation.pdf.gz | 919.2 KB | Display | |
Data in XML | 6xjn_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 6xjn_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/6xjn ftp://data.pdbj.org/pub/pdb/validation_reports/xj/6xjn | 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: 50405.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Production host: Escherichia coli (E. coli) References: UniProt: Q8WXF7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.39 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.5 M sodium formate pH 7, crystals transferred to cryo solution supplemented with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 39278 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 47.89 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.078 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.735 / Num. unique obs: 5640 / CC1/2: 0.902 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→40.86 Å / SU ML: 0.2439 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8923 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40.86 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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