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Yorodumi- PDB-2qpt: Crystal structure of an EHD ATPase involved in membrane remodelling -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qpt | ||||||
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Title | Crystal structure of an EHD ATPase involved in membrane remodelling | ||||||
Components | EH DOMAIN-CONTAINING PROTEIN-2 | ||||||
Keywords | ENDOCYTOSIS / PROTEIN-NUCLEOTIDE COMPLEX / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of endocytic recycling / plasma membrane tubulation / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / intercellular bridge / positive regulation of myoblast fusion / cilium assembly / endocytic vesicle / caveola ...positive regulation of endocytic recycling / plasma membrane tubulation / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / intercellular bridge / positive regulation of myoblast fusion / cilium assembly / endocytic vesicle / caveola / protein localization to plasma membrane / endocytosis / recycling endosome membrane / microtubule cytoskeleton / early endosome / hydrolase activity / protein domain specific binding / calcium ion binding / GTP binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å | ||||||
Authors | Daumke, O. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Architectural and mechanistic insights into an EHD ATPase involved in membrane remodelling. Authors: Daumke, O. / Lundmark, R. / Vallis, Y. / Martens, S. / Butler, P.J. / McMahon, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qpt.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qpt.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/2qpt ftp://data.pdbj.org/pub/pdb/validation_reports/qp/2qpt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second molecule of the EHD2 dimer is generated by the two fold crystallographic axis. |
-Components
#1: Protein | Mass: 61827.023 Da / Num. of mol.: 1 / Mutation: Q410A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ehd2 / Plasmid: pSKB-LNB / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 Rosetta / References: UniProt: Q8BH64 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-ANP / |
#5: 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: 2.93 Å3/Da / Density % sol: 58.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 3% PEG2000 MME, 50mM MES, 4mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97962 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2005 Details: DOUBLE CRYSTAL MONOCHROMATOR AND A TOROIDAL FOCUSING MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97962 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 12251 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.0708 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 4.5 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.1→19.96 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.885 / SU B: 50.779 / SU ML: 0.431 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC WITH TLS REFINEMENT / Cross valid method: THROUGHOUT / ESU R Free: 0.491 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.34 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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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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