+Open data
-Basic information
Entry | Database: PDB / ID: 2x2f | ||||||
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Title | Dynamin 1 GTPase dimer, short axis form | ||||||
Components | DYNAMIN-1 | ||||||
Keywords | HYDROLASE / NITRATION / MEMBRANE FISSION / NUCLEOTIDE-BINDING / ENDOCYTOSIS / MOTOR PROTEIN | ||||||
Function / homology | Function and homology information clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / photoreceptor ribbon synapse / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / dynamin GTPase / chromaffin granule / regulation of vesicle size / photoreceptor ribbon synapse / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / membrane coat / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / synaptic vesicle endocytosis / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / endocytosis / GDP binding / : / presynapse / Clathrin-mediated endocytosis / microtubule binding / protein homotetramerization / microtubule / GTPase activity / glutamatergic synapse / GTP binding / protein kinase binding / protein homodimerization activity / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chappie, J.S. / Acharya, S. / Leonard, M. / Schmid, S.L. / Dyda, F. | ||||||
Citation | Journal: Nature / Year: 2010 Title: G Domain Dimerization Controls Dynamin'S Assembly-Stimulated Gtpase Activity. Authors: Chappie, J.S. / Acharya, S. / Leonard, M. / Schmid, S.L. / Dyda, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x2f.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x2f.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 2x2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/2x2f ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x2f | HTTPS FTP |
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-Related structure data
Related structure data | 2x2eSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.994728, 0.102534, -0.001898), Vector: |
-Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 39764.117 Da / Num. of mol.: 2 Fragment: GTPASE DOMAIN, RESIDUES 6-320, GTPASE EFFECTOR DOMAIN, RESIDUES 726-750 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05193, dynamin GTPase |
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-Non-polymers , 5 types, 329 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE ASP-ASN CONFLICT BELOW HAS BEEN DESCRIBED AS A NATURAL VARIANT REFERRED BY SNP RS1042007 (PMID: 8101525). |
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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: 1.97 Å3/Da / Density % sol: 37.8 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING DROP VAPOR DIFFUSION IN 0.1M TRIS PH 8.5, 25% PEG 3350, 200MM NACL, 25-35% NAF USING A DROP SIZE OF 2-10 MICROL AND A RESERVOIR VOLUME OF 750 MICROL. CRYSTALS GREW IN 4-5 DAYS AT EITHER 17C OR 20C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979261 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 19, 2009 Details: SAGGITALY FOCUSING MONOCHROMATOR, REFLECTING MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979261 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 42969 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.02 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.89 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 10.1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X2E Resolution: 2→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 18.14 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO |