+Open data
-Basic information
Entry | Database: PDB / ID: 6b9e | ||||||
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Title | Human ATL1 mutant - R77A / F151S bound to GDP | ||||||
Components | Atlastin-1 | ||||||
Keywords | HYDROLASE / GTPase / dynamin related protein / hydrolysis-deficient | ||||||
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: 1.99 Å | ||||||
Authors | O'Donnell, J.P. / Sondermann, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: A hereditary spastic paraplegia-associated atlastin variant exhibits defective allosteric coupling in the catalytic core. Authors: O'Donnell, J.P. / Byrnes, L.J. / Cooley, R.B. / Sondermann, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b9e.cif.gz | 323.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b9e.ent.gz | 259.9 KB | Display | PDB format |
PDBx/mmJSON format | 6b9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b9e_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6b9e_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6b9e_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 6b9e_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/6b9e ftp://data.pdbj.org/pub/pdb/validation_reports/b9/6b9e | HTTPS FTP |
-Related structure data
Related structure data | 6b9dC 6b9fC 6b9gC 3q5eS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52442.246 Da / Num. of mol.: 2 / Fragment: residues 1-446 / Mutation: R77A, F151S 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 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.31 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris pH 5.5, 0.2 M ammonium sulfate, 22% PEG3350, 1 mM GDP, 2 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.631 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.631 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→42.75 Å / Num. obs: 60236 / % possible obs: 95.7 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.086 / Net I/σ(I): 9.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q5E Resolution: 1.99→13.85 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→13.85 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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