+Open data
-Basic information
Entry | Database: PDB / ID: 4cid | ||||||
---|---|---|---|---|---|---|---|
Title | Structural insights into the N-terminus of the EHD2 ATPase | ||||||
Components | EH DOMAIN-CONTAINING PROTEIN 2 | ||||||
Keywords | HYDROLASE / MECHANOCHEMICAL ATPASE / DYNAMIN SUPERFAMILY | ||||||
Function / homology | Function and homology information positive regulation of endocytic recycling / plasma membrane tubulation / clathrin coat of coated pit / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / positive regulation of myoblast fusion / intercellular bridge / endocytic vesicle / cilium assembly ...positive regulation of endocytic recycling / plasma membrane tubulation / clathrin coat of coated pit / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / positive regulation of myoblast fusion / intercellular bridge / endocytic vesicle / cilium assembly / caveola / protein localization to plasma membrane / recycling endosome membrane / endocytosis / microtubule cytoskeleton / early endosome / cadherin binding / hydrolase activity / protein domain specific binding / calcium ion binding / GTP binding / perinuclear region of cytoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Shah, C. / Daumke, O. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural Insights Into Membrane Interaction and Caveolar Targeting of Dynamin-Like Ehd2. Authors: Shah, C. / Hegde, B.G. / Mor, B. / Behrmann, E. / Mielke, T. / Moenke, G. / Spahn, C.M. / Lundmark, R. / Daumke, O. / Langen, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cid.cif.gz | 216.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cid.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 4cid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cid_validation.pdf.gz | 770.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4cid_full_validation.pdf.gz | 772.7 KB | Display | |
Data in XML | 4cid_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4cid_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/4cid ftp://data.pdbj.org/pub/pdb/validation_reports/ci/4cid | HTTPS FTP |
-Related structure data
Related structure data | 2qptS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 62642.273 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PSKB2-LNB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q8BH64, dynamin GTPase |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % Description: DATA COLLECTION STATISTICS ARE FOR THE ANOMALOUS DATA. EXPERIMENTAL (SEMET-DERIVED) PHASES DEPOSITED. |
---|---|
Crystal grow | pH: 6.5 / Details: 100 MM MES PH 6.5, 20 MM MGCL2, 4% PEG3350, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97969 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2010 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97969 Å / Relative weight: 1 |
Reflection | Resolution: 3→41 Å / Num. obs: 26426 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 1.63 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 98 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QPT Resolution: 3→78.15 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.904 / SU B: 53.277 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES HAVE BEEN ADDED WITH TLS. EXPERIMENTAL (SEMET-DERIVED) PHASES USED FOR REFINEMENT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 83.356 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→78.15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|