+Open data
-Basic information
Entry | Database: PDB / ID: 3w6o | ||||||
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Title | Crystal structure of human Dlp1 in complex with GMP-PCP | ||||||
Components | Dynamin-1-like protein | ||||||
Keywords | HYDROLASE / DNM1L / GTPASE / MEMBRANE FISSION / MITOCHONDRIAL FISSION / MICROTUBULE / NUCLEOTIDE-BINDING / MOTOR PROTEIN | ||||||
Function / homology | Function and homology information mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding / regulation of autophagy of mitochondrion ...mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / GTP-dependent protein binding / regulation of autophagy of mitochondrion / protein localization to mitochondrion / mitochondrial fission / positive regulation of neutrophil chemotaxis / regulation of mitochondrion organization / : / positive regulation of mitochondrial fission / intracellular distribution of mitochondria / heart contraction / positive regulation of release of cytochrome c from mitochondria / necroptotic process / brush border / localization / clathrin-coated pit / mitochondrion organization / positive regulation of intrinsic apoptotic signaling pathway / GTPase activator activity / release of cytochrome c from mitochondria / positive regulation of protein secretion / synaptic vesicle membrane / small GTPase binding / peroxisome / endocytosis / rhythmic process / calcium ion transport / protein complex oligomerization / regulation of gene expression / microtubule binding / protein-containing complex assembly / mitochondrial outer membrane / microtubule / membrane fusion / molecular adaptor activity / positive regulation of apoptotic process / intracellular membrane-bounded organelle / GTPase activity / lipid binding / ubiquitin protein ligase binding / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kishida, H. / Sugio, S. | ||||||
Citation | Journal: CURR TOP PEPT PROTEIN RES. / Year: 2013 Title: Crystal structure of GTPase domain fused with minimal stalks from human dynamin-1-like protein (Dlp1) in complex with several nucleotide analogues Authors: Kishida, H. / Sugio, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w6o.cif.gz | 161.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w6o.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/3w6o ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w6o | HTTPS FTP |
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-Related structure data
Related structure data | 3w6nSC 3w6pC 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40542.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CHIMERA PROTEIN OF UNP RESIDUES 1-329 AND 709-736 FROM UNIPROT O00429, LINKED WITH LINKER RESIDUES HGTDS. Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1L, DLP1, DRP1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O00429, dynamin GTPase |
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-Non-polymers , 5 types, 546 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: 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: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 550 MME, 0.05M calcium chloride, 0.1M Bis-Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 15, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 57544 / Num. obs: 57254 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 4.6 / Num. unique all: 4198 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W6N Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.734 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.291 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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